Starting phenix.real_space_refine on Wed Jan 17 20:06:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/01_2024/7t4k_25678_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/01_2024/7t4k_25678.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/01_2024/7t4k_25678.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/01_2024/7t4k_25678.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/01_2024/7t4k_25678_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4k_25678/01_2024/7t4k_25678_updated.pdb" } resolution = 3.25 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 41 5.16 5 C 3941 2.51 5 N 1048 2.21 5 O 1148 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 471": "OD1" <-> "OD2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "B TYR 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 222": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 379": "OD1" <-> "OD2" Residue "B GLU 492": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 6180 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 3039 Classifications: {'peptide': 379} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 361} Chain breaks: 5 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 25 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "B" Number of atoms: 3141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 3141 Classifications: {'peptide': 403} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 22, 'TRANS': 380} Chain breaks: 4 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 114 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 1, 'TYR:plan': 3, 'ASN:plan1': 3, 'ASP:plan': 1, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 67 Time building chain proxies: 3.90, per 1000 atoms: 0.63 Number of scatterers: 6180 At special positions: 0 Unit cell: (115.44, 78, 73.32, 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 41 16.00 P 2 15.00 O 1148 8.00 N 1048 7.00 C 3941 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: 2.39 Conformation dependent library (CDL) restraints added in 1.2 seconds 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1514 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 7 sheets defined 38.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.38 Creating SS restraints... Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'A' and resid 204 through 217 removed outlier: 4.435A pdb=" N VAL A 216 " --> pdb=" O TYR A 212 " (cutoff:3.500A) Proline residue: A 217 - end of helix 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: 3.564A pdb=" N ALA A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 472 through 484 removed outlier: 3.531A pdb=" N LEU A 483 " --> pdb=" O ALA A 479 " (cutoff:3.500A) 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 554 Processing helix chain 'A' and resid 558 through 573 Processing helix chain 'B' and resid 123 through 137 removed outlier: 3.737A pdb=" N GLY B 126 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA B 134 " --> pdb=" O ILE B 131 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N VAL B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LYS B 137 " --> pdb=" O ALA B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 263 through 266 No H-bonds generated for 'chain 'B' and resid 263 through 266' Processing helix chain 'B' and resid 268 through 270 No H-bonds generated for 'chain 'B' and resid 268 through 270' Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 337 through 339 No H-bonds generated for 'chain 'B' and resid 337 through 339' 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: 3.895A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) 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 554 Processing helix chain 'B' and resid 558 through 573 Processing sheet with id= A, first strand: chain 'A' and resid 171 through 176 removed outlier: 3.721A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA A 254 " --> pdb=" O PHE A 222 " (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: 3.558A pdb=" N LYS B 177 " --> pdb=" O ASP B 160 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 286 " --> pdb=" O MET B 195 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 340 through 343 Processing sheet with id= F, first strand: chain 'B' and resid 370 through 372 Processing sheet with id= G, first strand: chain 'B' and resid 164 through 167 removed outlier: 7.052A pdb=" N VAL B 173 " --> pdb=" O ILE B 165 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 618 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: 1.53 Time building geometry restraints manager: 2.62 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: 1988 1.34 - 1.46: 1125 1.46 - 1.58: 3112 1.58 - 1.69: 8 1.69 - 1.81: 65 Bond restraints: 6298 Sorted by residual: bond pdb=" C VAL B 216 " pdb=" N PRO B 217 " ideal model delta sigma weight residual 1.334 1.374 -0.041 2.34e-02 1.83e+03 3.00e+00 bond pdb=" C LEU A 543 " pdb=" N PRO A 544 " ideal model delta sigma weight residual 1.334 1.359 -0.024 1.51e-02 4.39e+03 2.60e+00 bond pdb=" CB ASP B 442 " pdb=" CG ASP B 442 " ideal model delta sigma weight residual 1.516 1.476 0.040 2.50e-02 1.60e+03 2.50e+00 bond pdb=" CG LEU A 571 " pdb=" CD1 LEU A 571 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.47e+00 bond pdb=" C LEU B 543 " pdb=" N PRO B 544 " ideal model delta sigma weight residual 1.335 1.354 -0.020 1.28e-02 6.10e+03 2.35e+00 ... (remaining 6293 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.10: 137 105.10 - 112.35: 3168 112.35 - 119.60: 2152 119.60 - 126.85: 2986 126.85 - 134.10: 89 Bond angle restraints: 8532 Sorted by residual: angle pdb=" CA GLU A 214 " pdb=" CB GLU A 214 " pdb=" CG GLU A 214 " ideal model delta sigma weight residual 114.10 122.48 -8.38 2.00e+00 2.50e-01 1.75e+01 angle pdb=" CA MET B 249 " pdb=" CB MET B 249 " pdb=" CG MET B 249 " ideal model delta sigma weight residual 114.10 122.10 -8.00 2.00e+00 2.50e-01 1.60e+01 angle pdb=" N GLU B 441 " pdb=" CA GLU B 441 " pdb=" C GLU B 441 " ideal model delta sigma weight residual 111.36 115.39 -4.03 1.09e+00 8.42e-01 1.37e+01 angle pdb=" CB MET B 195 " pdb=" CG MET B 195 " pdb=" SD MET B 195 " ideal model delta sigma weight residual 112.70 101.71 10.99 3.00e+00 1.11e-01 1.34e+01 angle pdb=" CB GLN A 569 " pdb=" CG GLN A 569 " pdb=" CD GLN A 569 " ideal model delta sigma weight residual 112.60 118.81 -6.21 1.70e+00 3.46e-01 1.33e+01 ... (remaining 8527 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.79: 3498 16.79 - 33.58: 296 33.58 - 50.37: 46 50.37 - 67.16: 7 67.16 - 83.95: 6 Dihedral angle restraints: 3853 sinusoidal: 1537 harmonic: 2316 Sorted by residual: dihedral pdb=" CA SER B 280 " pdb=" C SER B 280 " pdb=" N GLY B 281 " pdb=" CA GLY B 281 " ideal model delta harmonic sigma weight residual -180.00 -162.06 -17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA ASN A 326 " pdb=" CB ASN A 326 " pdb=" CG ASN A 326 " pdb=" OD1 ASN A 326 " ideal model delta sinusoidal sigma weight residual 120.00 -173.25 -66.75 2 2.00e+01 2.50e-03 1.01e+01 dihedral pdb=" CA ASP B 121 " pdb=" CB ASP B 121 " pdb=" CG ASP B 121 " pdb=" OD1 ASP B 121 " ideal model delta sinusoidal sigma weight residual -30.00 -84.01 54.01 1 2.00e+01 2.50e-03 9.90e+00 ... (remaining 3850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 693 0.048 - 0.095: 201 0.095 - 0.143: 61 0.143 - 0.191: 14 0.191 - 0.239: 2 Chirality restraints: 971 Sorted by residual: chirality pdb=" CA GLU A 158 " pdb=" N GLU A 158 " pdb=" C GLU A 158 " pdb=" CB GLU A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+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 2.64 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA ILE B 257 " pdb=" N ILE B 257 " pdb=" C ILE B 257 " pdb=" CB ILE B 257 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.70e-01 ... (remaining 968 not shown) Planarity restraints: 1080 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 439 " 0.013 2.00e-02 2.50e+03 2.56e-02 6.58e+00 pdb=" C LYS B 439 " -0.044 2.00e-02 2.50e+03 pdb=" O LYS B 439 " 0.017 2.00e-02 2.50e+03 pdb=" N GLU B 440 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 125 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C GLU B 125 " 0.037 2.00e-02 2.50e+03 pdb=" O GLU B 125 " -0.014 2.00e-02 2.50e+03 pdb=" N GLY B 126 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 129 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.86e+00 pdb=" C TRP B 129 " -0.034 2.00e-02 2.50e+03 pdb=" O TRP B 129 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU B 130 " 0.011 2.00e-02 2.50e+03 ... (remaining 1077 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 1574 2.81 - 3.33: 5766 3.33 - 3.85: 9649 3.85 - 4.38: 11796 4.38 - 4.90: 20271 Nonbonded interactions: 49056 Sorted by model distance: nonbonded pdb=" OE2 GLU B 346 " pdb=" OG1 THR B 352 " model vdw 2.287 2.440 nonbonded pdb=" ND2 ASN B 197 " pdb=" O MET B 284 " model vdw 2.361 2.520 nonbonded pdb=" OE2 GLU A 320 " pdb=" NH2 ARG A 555 " model vdw 2.379 2.520 nonbonded pdb=" OE2 GLU B 320 " pdb=" NH2 ARG B 555 " model vdw 2.388 2.520 nonbonded pdb=" O TYR B 212 " pdb=" NH1 ARG B 239 " model vdw 2.397 2.520 ... (remaining 49051 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 200 or (resid 201 and (name N or name CA or name C or n \ ame O or name CB )) or resid 202 through 223 or (resid 237 and (name N or name C \ A or name C or name O or name CB )) or resid 238 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 282 and \ (name N or name CA or name C or name O or name CB )) or resid 283 through 511 o \ r 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: 4.650 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: 0.000 Extract box with map and model: 17.160 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 20.650 Find NCS groups from input model: 0.350 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:2.570 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 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 0.070 6298 Z= 0.302 Angle : 0.881 11.701 8532 Z= 0.468 Chirality : 0.051 0.239 971 Planarity : 0.006 0.046 1080 Dihedral : 12.764 83.950 2339 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.15 % Allowed : 1.20 % Favored : 98.65 % 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: 0.51 (0.30), residues: 754 helix: 1.27 (0.28), residues: 298 sheet: -0.64 (0.49), residues: 114 loop : -0.02 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 567 HIS 0.005 0.001 HIS B 559 PHE 0.032 0.002 PHE B 222 TYR 0.030 0.002 TYR A 373 ARG 0.010 0.001 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.760 Fit side-chains REVERT: A 214 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7845 (mm-30) outliers start: 1 outliers final: 0 residues processed: 99 average time/residue: 0.1571 time to fit residues: 21.5392 Evaluate side-chains 82 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 65 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 36 optimal weight: 0.0980 chunk 44 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN B 366 GLN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.0969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6298 Z= 0.229 Angle : 0.496 6.288 8532 Z= 0.253 Chirality : 0.039 0.146 971 Planarity : 0.004 0.036 1080 Dihedral : 5.799 78.171 847 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 1.50 % Allowed : 5.40 % Favored : 93.10 % 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: 1.26 (0.30), residues: 754 helix: 2.07 (0.28), residues: 304 sheet: -0.42 (0.47), residues: 114 loop : 0.25 (0.34), residues: 336 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 0.009 0.001 PHE A 253 TYR 0.015 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.732 Fit side-chains REVERT: A 167 LYS cc_start: 0.8046 (mptt) cc_final: 0.7732 (mttp) REVERT: B 189 GLN cc_start: 0.7742 (mm-40) cc_final: 0.7525 (mm110) outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 0.1629 time to fit residues: 20.4764 Evaluate side-chains 86 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 571 LEU Chi-restraints excluded: chain B residue 573 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 38 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 58 optimal weight: 0.0040 chunk 47 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 chunk 75 optimal weight: 0.0970 chunk 62 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 56 optimal weight: 1.9990 overall best weight: 0.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN B 366 GLN B 504 GLN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6298 Z= 0.175 Angle : 0.448 5.671 8532 Z= 0.229 Chirality : 0.038 0.140 971 Planarity : 0.004 0.034 1080 Dihedral : 5.725 77.329 847 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.20 % Allowed : 7.80 % Favored : 91.00 % 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: 754 helix: 2.40 (0.29), residues: 306 sheet: -0.23 (0.48), residues: 114 loop : 0.36 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 401 HIS 0.003 0.001 HIS B 559 PHE 0.009 0.001 PHE A 253 TYR 0.013 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.778 Fit side-chains REVERT: A 167 LYS cc_start: 0.8026 (mptt) cc_final: 0.7676 (mttp) REVERT: B 189 GLN cc_start: 0.7727 (mm-40) cc_final: 0.7503 (mm110) outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 0.1586 time to fit residues: 18.8061 Evaluate side-chains 82 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 77 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 571 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 69 optimal weight: 0.0770 chunk 52 optimal weight: 0.0370 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 70 optimal weight: 0.0170 chunk 74 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.2854 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN B 170 ASN B 366 GLN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6298 Z= 0.151 Angle : 0.433 5.018 8532 Z= 0.221 Chirality : 0.038 0.137 971 Planarity : 0.004 0.033 1080 Dihedral : 5.669 76.365 847 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.65 % Allowed : 8.40 % Favored : 89.96 % 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: 1.75 (0.31), residues: 754 helix: 2.51 (0.29), residues: 306 sheet: -0.12 (0.47), residues: 114 loop : 0.46 (0.35), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP A 401 HIS 0.002 0.001 HIS B 559 PHE 0.010 0.001 PHE A 253 TYR 0.011 0.001 TYR B 482 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.671 Fit side-chains REVERT: A 167 LYS cc_start: 0.8032 (mptt) cc_final: 0.7658 (mttp) REVERT: A 214 GLU cc_start: 0.8142 (mm-30) cc_final: 0.7618 (tp30) REVERT: B 189 GLN cc_start: 0.7709 (mm-40) cc_final: 0.7507 (mm110) outliers start: 11 outliers final: 9 residues processed: 82 average time/residue: 0.1542 time to fit residues: 17.7432 Evaluate side-chains 83 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 74 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 571 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 42 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 66 optimal weight: 0.7980 chunk 18 optimal weight: 0.0030 chunk 25 optimal weight: 0.0470 overall best weight: 0.4888 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 366 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6298 Z= 0.209 Angle : 0.455 7.019 8532 Z= 0.230 Chirality : 0.038 0.139 971 Planarity : 0.004 0.035 1080 Dihedral : 5.653 74.463 847 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.10 % Allowed : 9.30 % Favored : 88.61 % 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: 1.74 (0.31), residues: 754 helix: 2.47 (0.29), residues: 307 sheet: -0.15 (0.47), residues: 115 loop : 0.50 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 505 HIS 0.003 0.001 HIS B 332 PHE 0.010 0.001 PHE A 253 TYR 0.014 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 75 time to evaluate : 0.751 Fit side-chains REVERT: A 167 LYS cc_start: 0.8022 (mptt) cc_final: 0.7630 (mttp) REVERT: A 214 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7732 (tp30) REVERT: B 471 ASP cc_start: 0.8095 (OUTLIER) cc_final: 0.7892 (p0) outliers start: 14 outliers final: 7 residues processed: 80 average time/residue: 0.1683 time to fit residues: 18.6927 Evaluate side-chains 83 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 471 ASP Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 571 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 67 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 74 optimal weight: 0.4980 chunk 61 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 71 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN B 366 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6298 Z= 0.252 Angle : 0.469 5.259 8532 Z= 0.235 Chirality : 0.039 0.140 971 Planarity : 0.004 0.036 1080 Dihedral : 5.664 74.579 847 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.40 % Allowed : 9.45 % Favored : 88.16 % 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: 1.67 (0.31), residues: 754 helix: 2.40 (0.29), residues: 307 sheet: -0.26 (0.46), residues: 115 loop : 0.51 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 505 HIS 0.004 0.001 HIS B 332 PHE 0.009 0.001 PHE A 287 TYR 0.016 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 0.775 Fit side-chains REVERT: A 167 LYS cc_start: 0.8072 (mptt) cc_final: 0.7667 (mttp) REVERT: A 214 GLU cc_start: 0.8220 (mm-30) cc_final: 0.7539 (tp30) REVERT: A 360 CYS cc_start: 0.7965 (m) cc_final: 0.7748 (m) REVERT: B 150 GLN cc_start: 0.7266 (mp10) cc_final: 0.7038 (pm20) outliers start: 16 outliers final: 11 residues processed: 85 average time/residue: 0.1689 time to fit residues: 19.6164 Evaluate side-chains 83 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 571 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 8 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 45 optimal weight: 0.0470 chunk 34 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6298 Z= 0.218 Angle : 0.466 5.287 8532 Z= 0.234 Chirality : 0.038 0.139 971 Planarity : 0.003 0.034 1080 Dihedral : 5.607 74.479 847 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.40 % Allowed : 10.19 % Favored : 87.41 % 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: 1.65 (0.31), residues: 754 helix: 2.37 (0.29), residues: 307 sheet: -0.24 (0.47), residues: 110 loop : 0.46 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 505 HIS 0.003 0.001 HIS B 332 PHE 0.009 0.001 PHE A 452 TYR 0.013 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.757 Fit side-chains REVERT: A 167 LYS cc_start: 0.8059 (mptt) cc_final: 0.7799 (mttp) REVERT: A 214 GLU cc_start: 0.8202 (mm-30) cc_final: 0.7530 (tp30) REVERT: B 150 GLN cc_start: 0.7280 (mp10) cc_final: 0.7075 (pm20) outliers start: 16 outliers final: 9 residues processed: 83 average time/residue: 0.1545 time to fit residues: 18.1044 Evaluate side-chains 84 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 75 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain A residue 572 HIS Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 205 THR Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 22 optimal weight: 0.3980 chunk 14 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 50 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 64 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6298 Z= 0.279 Angle : 0.499 5.674 8532 Z= 0.250 Chirality : 0.040 0.140 971 Planarity : 0.004 0.037 1080 Dihedral : 5.557 73.616 847 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.95 % Allowed : 11.24 % Favored : 86.81 % 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: 1.49 (0.31), residues: 754 helix: 2.25 (0.29), residues: 307 sheet: -0.09 (0.48), residues: 101 loop : 0.26 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 505 HIS 0.004 0.001 HIS B 332 PHE 0.009 0.001 PHE A 452 TYR 0.015 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.769 Fit side-chains REVERT: A 167 LYS cc_start: 0.8105 (mptt) cc_final: 0.7847 (mttp) REVERT: A 214 GLU cc_start: 0.8237 (mm-30) cc_final: 0.7580 (tp30) outliers start: 13 outliers final: 8 residues processed: 84 average time/residue: 0.1753 time to fit residues: 20.0682 Evaluate side-chains 83 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain A residue 325 MET Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 71 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 30 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 65 optimal weight: 0.1980 chunk 68 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6298 Z= 0.205 Angle : 0.504 8.047 8532 Z= 0.252 Chirality : 0.039 0.139 971 Planarity : 0.003 0.035 1080 Dihedral : 5.464 73.413 847 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.65 % Allowed : 12.14 % Favored : 86.21 % 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: 1.53 (0.31), residues: 754 helix: 2.28 (0.29), residues: 307 sheet: -0.06 (0.48), residues: 101 loop : 0.29 (0.34), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 567 HIS 0.003 0.001 HIS A 572 PHE 0.009 0.001 PHE B 452 TYR 0.012 0.001 TYR B 482 ARG 0.002 0.000 ARG B 555 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 76 time to evaluate : 0.705 Fit side-chains REVERT: A 167 LYS cc_start: 0.8093 (mptt) cc_final: 0.7822 (mttp) REVERT: A 214 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7497 (tp30) REVERT: A 357 ASP cc_start: 0.7853 (t0) cc_final: 0.7254 (t0) outliers start: 11 outliers final: 8 residues processed: 80 average time/residue: 0.1588 time to fit residues: 17.8401 Evaluate side-chains 84 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 76 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 70 optimal weight: 0.4980 chunk 61 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 48 optimal weight: 0.0170 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6298 Z= 0.242 Angle : 0.505 8.022 8532 Z= 0.251 Chirality : 0.039 0.140 971 Planarity : 0.004 0.036 1080 Dihedral : 5.397 73.574 847 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 1.35 % Allowed : 12.74 % Favored : 85.91 % 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: 1.47 (0.31), residues: 754 helix: 2.23 (0.30), residues: 307 sheet: -0.07 (0.49), residues: 100 loop : 0.25 (0.34), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 505 HIS 0.003 0.001 HIS B 332 PHE 0.009 0.001 PHE A 452 TYR 0.013 0.001 TYR A 373 ARG 0.003 0.000 ARG B 555 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1508 Ramachandran restraints generated. 754 Oldfield, 0 Emsley, 754 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 71 time to evaluate : 0.754 Fit side-chains REVERT: A 167 LYS cc_start: 0.8095 (mptt) cc_final: 0.7836 (mttp) REVERT: A 214 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7552 (tp30) outliers start: 9 outliers final: 8 residues processed: 77 average time/residue: 0.1686 time to fit residues: 18.3393 Evaluate side-chains 77 residues out of total 702 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 69 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ILE Chi-restraints excluded: chain A residue 235 ASP Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 434 LEU Chi-restraints excluded: chain B residue 449 THR Chi-restraints excluded: chain B residue 515 CYS Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 560 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 77 random chunks: chunk 56 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 62 optimal weight: 0.3980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.0970 chunk 53 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 152 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.101784 restraints weight = 8675.294| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.97 r_work: 0.3035 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6298 Z= 0.199 Angle : 0.496 8.547 8532 Z= 0.246 Chirality : 0.038 0.139 971 Planarity : 0.003 0.035 1080 Dihedral : 5.320 72.045 847 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.50 % Allowed : 12.74 % Favored : 85.76 % 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: 1.49 (0.31), residues: 754 helix: 2.25 (0.29), residues: 308 sheet: 0.01 (0.49), residues: 100 loop : 0.22 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 567 HIS 0.003 0.001 HIS B 332 PHE 0.011 0.001 PHE A 287 TYR 0.012 0.001 TYR B 482 ARG 0.002 0.000 ARG B 555 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1818.73 seconds wall clock time: 33 minutes 33.34 seconds (2013.34 seconds total)