Starting phenix.real_space_refine on Fri Dec 8 01:26:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/12_2023/7t4n_25681.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/12_2023/7t4n_25681.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/12_2023/7t4n_25681.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/12_2023/7t4n_25681.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/12_2023/7t4n_25681.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4n_25681/12_2023/7t4n_25681.pdb" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 44 5.16 5 C 4148 2.51 5 N 1090 2.21 5 O 1194 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 199": "OD1" <-> "OD2" Residue "A ASP 235": "OD1" <-> "OD2" Residue "A PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 338": "OD1" <-> "OD2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ASP 348": "OD1" <-> "OD2" Residue "A ASP 379": "OD1" <-> "OD2" Residue "A PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 445": "OE1" <-> "OE2" Residue "B GLU 149": "OE1" <-> "OE2" Residue "B ASP 157": "OD1" <-> "OD2" Residue "B GLU 158": "OE1" <-> "OE2" Residue "B PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 377": "OD1" <-> "OD2" Residue "B ASP 428": "OD1" <-> "OD2" Residue "B GLU 441": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 6476 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3264 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 404, 3255 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Conformer: "B" Number of residues, atoms: 404, 3255 Classifications: {'peptide': 404} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 385} Chain breaks: 4 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 bond proxies already assigned to first conformer: 3308 Chain: "B" Number of atoms: 3212 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 399, 3203 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 399, 3203 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 380} Chain breaks: 4 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3255 Time building chain proxies: 6.26, per 1000 atoms: 0.97 Number of scatterers: 6476 At special positions: 0 Unit cell: (115.787, 78.302, 74.97, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 44 16.00 O 1194 8.00 N 1090 7.00 C 4148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 2.1 seconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1564 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 8 sheets defined 44.3% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 119 through 137 Processing helix chain 'A' and resid 155 through 157 No H-bonds generated for 'chain 'A' and resid 155 through 157' Processing helix chain 'A' and resid 203 through 215 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 307 through 328 Processing helix chain 'A' and resid 357 through 361 removed outlier: 4.566A pdb=" N CYS A 360 " --> pdb=" O ALA A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 393 Processing helix chain 'A' and resid 406 through 420 removed outlier: 3.589A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 443 Processing helix chain 'A' and resid 451 through 462 Processing helix chain 'A' and resid 471 through 485 Processing helix chain 'A' and resid 486 through 491 removed outlier: 3.990A pdb=" N LEU A 490 " --> pdb=" O PRO A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 515 Processing helix chain 'A' and resid 542 through 554 Processing helix chain 'A' and resid 557 through 574 removed outlier: 4.022A pdb=" N HIS A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 573 " --> pdb=" O GLN A 569 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 137 removed outlier: 4.164A pdb=" N GLY B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ILE B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N CYS B 128 " --> pdb=" O LEU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 removed outlier: 3.724A pdb=" N GLU B 158 " --> pdb=" O ASN B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 215 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 307 through 328 removed outlier: 3.587A pdb=" N HIS B 328 " --> pdb=" O HIS B 324 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 361 removed outlier: 4.536A pdb=" N CYS B 360 " --> pdb=" O ALA B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 393 Processing helix chain 'B' and resid 406 through 420 removed outlier: 3.733A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 443 removed outlier: 3.515A pdb=" N LEU B 443 " --> pdb=" O GLU B 440 " (cutoff:3.500A) Processing helix chain 'B' and resid 451 through 462 Processing helix chain 'B' and resid 471 through 485 Processing helix chain 'B' and resid 486 through 491 removed outlier: 3.779A pdb=" N LEU B 490 " --> pdb=" O PRO B 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 515 Processing helix chain 'B' and resid 542 through 554 Processing helix chain 'B' and resid 557 through 574 removed outlier: 3.819A pdb=" N HIS B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 160 removed outlier: 3.573A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 295 through 296 Processing sheet with id=AA4, first strand: chain 'A' and resid 330 through 331 Processing sheet with id=AA5, first strand: chain 'A' and resid 370 through 372 Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 166 removed outlier: 7.056A pdb=" N LYS B 291 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N MET B 249 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 295 through 296 removed outlier: 3.528A pdb=" N CYS B 295 " --> pdb=" O VAL B 342 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 370 through 372 293 hydrogen bonds defined for protein. 841 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: 1.91 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2087 1.34 - 1.46: 1313 1.46 - 1.58: 3139 1.58 - 1.69: 0 1.69 - 1.81: 68 Bond restraints: 6607 Sorted by residual: bond pdb=" CB ASP B 428 " pdb=" CG ASP B 428 " ideal model delta sigma weight residual 1.516 1.540 -0.024 2.50e-02 1.60e+03 9.24e-01 bond pdb=" C ILE A 233 " pdb=" O ILE A 233 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.19e-02 7.06e+03 8.44e-01 bond pdb=" CB LYS B 432 " pdb=" CG LYS B 432 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.51e-01 bond pdb=" CG LYS B 432 " pdb=" CD LYS B 432 " ideal model delta sigma weight residual 1.520 1.541 -0.021 3.00e-02 1.11e+03 4.98e-01 bond pdb=" CA ASP B 428 " pdb=" CB ASP B 428 " ideal model delta sigma weight residual 1.528 1.540 -0.012 1.66e-02 3.63e+03 4.92e-01 ... (remaining 6602 not shown) Histogram of bond angle deviations from ideal: 100.20 - 106.97: 195 106.97 - 113.73: 3678 113.73 - 120.50: 2562 120.50 - 127.26: 2440 127.26 - 134.03: 71 Bond angle restraints: 8946 Sorted by residual: angle pdb=" CB LYS B 432 " pdb=" CG LYS B 432 " pdb=" CD LYS B 432 " ideal model delta sigma weight residual 111.30 117.10 -5.80 2.30e+00 1.89e-01 6.35e+00 angle pdb=" CA ASP B 428 " pdb=" CB ASP B 428 " pdb=" CG ASP B 428 " ideal model delta sigma weight residual 112.60 114.61 -2.01 1.00e+00 1.00e+00 4.03e+00 angle pdb=" CB ASP B 428 " pdb=" CG ASP B 428 " pdb=" OD1 ASP B 428 " ideal model delta sigma weight residual 118.40 122.72 -4.32 2.30e+00 1.89e-01 3.53e+00 angle pdb=" C ASP B 428 " pdb=" CA ASP B 428 " pdb=" CB ASP B 428 " ideal model delta sigma weight residual 109.65 112.58 -2.93 1.71e+00 3.42e-01 2.93e+00 angle pdb=" C SER B 175 " pdb=" N ALA B 176 " pdb=" CA ALA B 176 " ideal model delta sigma weight residual 122.29 119.88 2.41 1.65e+00 3.67e-01 2.13e+00 ... (remaining 8941 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.59: 3537 17.59 - 35.18: 377 35.18 - 52.78: 110 52.78 - 70.37: 15 70.37 - 87.96: 11 Dihedral angle restraints: 4050 sinusoidal: 1652 harmonic: 2398 Sorted by residual: 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 -89.26 59.26 1 2.00e+01 2.50e-03 1.17e+01 dihedral pdb=" CB GLU A 133 " pdb=" CG GLU A 133 " pdb=" CD GLU A 133 " pdb=" OE1 GLU A 133 " ideal model delta sinusoidal sigma weight residual 0.00 -87.96 87.96 1 3.00e+01 1.11e-03 1.03e+01 dihedral pdb=" CA GLN B 189 " pdb=" C GLN B 189 " pdb=" N LEU B 190 " pdb=" CA LEU B 190 " ideal model delta harmonic sigma weight residual 180.00 -164.22 -15.78 0 5.00e+00 4.00e-02 9.97e+00 ... (remaining 4047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 581 0.026 - 0.051: 274 0.051 - 0.077: 102 0.077 - 0.102: 29 0.102 - 0.128: 23 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA ILE B 450 " pdb=" N ILE B 450 " pdb=" C ILE B 450 " pdb=" CB ILE B 450 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 chirality pdb=" CA ILE A 165 " pdb=" N ILE A 165 " pdb=" C ILE A 165 " pdb=" CB ILE A 165 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 chirality pdb=" CA VAL B 252 " pdb=" N VAL B 252 " pdb=" C VAL B 252 " pdb=" CB VAL B 252 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 ... (remaining 1006 not shown) Planarity restraints: 1134 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 401 " 0.008 2.00e-02 2.50e+03 7.94e-03 1.58e+00 pdb=" CG TRP A 401 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP A 401 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 401 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 401 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 401 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 401 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 401 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 401 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 401 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE A 450 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO A 451 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 451 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 451 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 450 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO B 451 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO B 451 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO B 451 " -0.016 5.00e-02 4.00e+02 ... (remaining 1131 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 571 2.75 - 3.28: 6256 3.28 - 3.82: 10918 3.82 - 4.36: 14131 4.36 - 4.90: 22842 Nonbonded interactions: 54718 Sorted by model distance: nonbonded pdb=" OH TYR B 438 " pdb=" O LEU B 462 " model vdw 2.207 2.440 nonbonded pdb=" O ARG B 132 " pdb=" OG SER B 136 " model vdw 2.219 2.440 nonbonded pdb=" OH TYR A 438 " pdb=" O LEU A 462 " model vdw 2.224 2.440 nonbonded pdb=" O GLY A 382 " pdb=" OG1 THR B 205 " model vdw 2.254 2.440 nonbonded pdb=" OD1 ASP B 428 " pdb=" N THR B 430 " model vdw 2.299 2.520 ... (remaining 54713 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 179 or resid 188 through 211 or resid 213 through 267 o \ r (resid 282 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 83 through 573 or (resid 574 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'B' and (resid 120 through 211 or resid 213 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=0.50 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: 5.490 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: 11.190 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 24.110 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:18.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 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 : 0.002 0.032 6607 Z= 0.149 Angle : 0.423 5.798 8946 Z= 0.222 Chirality : 0.038 0.128 1009 Planarity : 0.003 0.030 1134 Dihedral : 16.225 87.960 2486 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.25 % Allowed : 17.48 % Favored : 81.28 % 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: 0.87 (0.28), residues: 785 helix: 1.35 (0.28), residues: 320 sheet: 0.50 (0.51), residues: 105 loop : -0.01 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 401 HIS 0.002 0.001 HIS B 328 PHE 0.011 0.001 PHE A 253 TYR 0.009 0.001 TYR B 482 ARG 0.005 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.763 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 110 average time/residue: 1.0988 time to fit residues: 126.6668 Evaluate side-chains 108 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 103 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.6235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 189 GLN A 283 ASN A 366 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.0751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6607 Z= 0.257 Angle : 0.514 4.846 8946 Z= 0.275 Chirality : 0.041 0.141 1009 Planarity : 0.004 0.032 1134 Dihedral : 4.180 15.219 873 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 3.05 % Allowed : 15.26 % Favored : 81.69 % 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: 1.18 (0.29), residues: 785 helix: 1.82 (0.28), residues: 327 sheet: 0.43 (0.49), residues: 105 loop : -0.01 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 401 HIS 0.004 0.001 HIS A 324 PHE 0.014 0.002 PHE A 253 TYR 0.016 0.002 TYR A 482 ARG 0.006 0.001 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 102 time to evaluate : 0.778 Fit side-chains outliers start: 22 outliers final: 12 residues processed: 114 average time/residue: 1.2471 time to fit residues: 149.2554 Evaluate side-chains 110 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.753 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 9 residues processed: 3 average time/residue: 0.8691 time to fit residues: 3.8508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 71 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 64 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 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: 0.8242 moved from start: 0.0897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6607 Z= 0.211 Angle : 0.480 4.686 8946 Z= 0.256 Chirality : 0.040 0.141 1009 Planarity : 0.004 0.041 1134 Dihedral : 4.145 15.865 873 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 3.33 % Allowed : 15.40 % Favored : 81.28 % 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: 1.29 (0.29), residues: 785 helix: 1.99 (0.28), residues: 327 sheet: 0.42 (0.49), residues: 105 loop : -0.03 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 401 HIS 0.003 0.001 HIS A 559 PHE 0.015 0.002 PHE A 253 TYR 0.014 0.001 TYR B 482 ARG 0.008 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 101 time to evaluate : 1.603 Fit side-chains outliers start: 24 outliers final: 11 residues processed: 117 average time/residue: 1.3549 time to fit residues: 166.6255 Evaluate side-chains 115 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 104 time to evaluate : 0.786 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.0597 time to fit residues: 3.7280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 48 optimal weight: 0.7980 chunk 72 optimal weight: 0.0060 chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 1 optimal weight: 0.1980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 189 GLN A 366 GLN A 504 GLN B 569 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6607 Z= 0.140 Angle : 0.441 4.591 8946 Z= 0.234 Chirality : 0.038 0.143 1009 Planarity : 0.004 0.039 1134 Dihedral : 3.931 16.849 873 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.36 % Allowed : 15.81 % Favored : 81.83 % 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: 1.51 (0.29), residues: 785 helix: 2.27 (0.28), residues: 327 sheet: 0.14 (0.47), residues: 115 loop : 0.15 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.015 0.001 PHE A 253 TYR 0.012 0.001 TYR B 482 ARG 0.010 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.789 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 11 residues processed: 117 average time/residue: 1.2705 time to fit residues: 155.9732 Evaluate side-chains 114 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.360 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.1527 time to fit residues: 3.4894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 0.0050 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 366 GLN A 504 GLN B 569 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6607 Z= 0.220 Angle : 0.482 4.656 8946 Z= 0.256 Chirality : 0.040 0.139 1009 Planarity : 0.004 0.038 1134 Dihedral : 4.123 17.622 873 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.91 % Allowed : 15.81 % Favored : 81.28 % 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: 1.39 (0.29), residues: 785 helix: 2.15 (0.28), residues: 327 sheet: 0.40 (0.49), residues: 105 loop : -0.03 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 401 HIS 0.004 0.001 HIS A 328 PHE 0.016 0.002 PHE A 253 TYR 0.016 0.001 TYR B 174 ARG 0.008 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 99 time to evaluate : 0.790 Fit side-chains outliers start: 21 outliers final: 11 residues processed: 112 average time/residue: 1.2638 time to fit residues: 148.8078 Evaluate side-chains 109 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.767 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.9454 time to fit residues: 5.1201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 40 optimal weight: 0.0010 chunk 73 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 366 GLN ** B 189 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.8231 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6607 Z= 0.179 Angle : 0.473 8.216 8946 Z= 0.248 Chirality : 0.039 0.140 1009 Planarity : 0.004 0.035 1134 Dihedral : 4.067 17.686 873 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 2.22 % Allowed : 16.50 % Favored : 81.28 % 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: 1.45 (0.29), residues: 785 helix: 2.23 (0.28), residues: 327 sheet: 0.07 (0.48), residues: 115 loop : 0.11 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.016 0.002 PHE A 253 TYR 0.014 0.001 TYR B 482 ARG 0.007 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.930 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 110 average time/residue: 1.3604 time to fit residues: 156.9661 Evaluate side-chains 109 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.1846 time to fit residues: 3.4798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 0.1980 chunk 64 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 46 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 155 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 366 GLN A 504 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: 0.8223 moved from start: 0.1129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6607 Z= 0.161 Angle : 0.464 7.980 8946 Z= 0.243 Chirality : 0.039 0.141 1009 Planarity : 0.004 0.034 1134 Dihedral : 3.983 17.777 873 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.50 % Allowed : 16.50 % Favored : 81.00 % 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: 1.52 (0.29), residues: 785 helix: 2.32 (0.28), residues: 327 sheet: 0.07 (0.48), residues: 115 loop : 0.12 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.016 0.002 PHE A 253 TYR 0.013 0.001 TYR B 482 ARG 0.007 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 99 time to evaluate : 0.717 Fit side-chains revert: symmetry clash outliers start: 18 outliers final: 13 residues processed: 112 average time/residue: 1.3035 time to fit residues: 153.4723 Evaluate side-chains 112 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 99 time to evaluate : 0.784 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 9 residues processed: 4 average time/residue: 1.2764 time to fit residues: 6.3910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.0570 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 69 optimal weight: 0.0870 chunk 72 optimal weight: 0.9980 chunk 66 optimal weight: 0.5980 chunk 70 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 366 GLN A 504 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6607 Z= 0.146 Angle : 0.454 7.888 8946 Z= 0.237 Chirality : 0.039 0.141 1009 Planarity : 0.004 0.032 1134 Dihedral : 3.904 17.504 873 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.94 % Allowed : 17.20 % Favored : 80.86 % 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: 1.57 (0.29), residues: 785 helix: 2.39 (0.28), residues: 327 sheet: 0.11 (0.48), residues: 115 loop : 0.13 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.015 0.001 PHE A 253 TYR 0.012 0.001 TYR B 482 ARG 0.007 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.795 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 112 average time/residue: 1.2288 time to fit residues: 144.6758 Evaluate side-chains 109 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 9 residues processed: 2 average time/residue: 1.1684 time to fit residues: 3.4975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 64 optimal weight: 0.0270 chunk 67 optimal weight: 0.1980 chunk 70 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 0.0970 chunk 45 optimal weight: 0.0970 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.4980 overall best weight: 0.1834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 366 GLN B 569 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6607 Z= 0.116 Angle : 0.435 7.870 8946 Z= 0.226 Chirality : 0.038 0.143 1009 Planarity : 0.003 0.031 1134 Dihedral : 3.695 16.921 873 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.25 % Allowed : 18.31 % Favored : 80.44 % 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 (0.29), residues: 785 helix: 2.48 (0.28), residues: 333 sheet: 0.14 (0.48), residues: 115 loop : 0.19 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 401 HIS 0.002 0.001 HIS A 328 PHE 0.014 0.001 PHE A 253 TYR 0.010 0.001 TYR B 174 ARG 0.007 0.000 ARG B 541 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.793 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 111 average time/residue: 1.2070 time to fit residues: 140.7644 Evaluate side-chains 107 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.759 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 7 residues processed: 0 time to fit residues: 1.0482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 0.5980 chunk 72 optimal weight: 0.6980 chunk 62 optimal weight: 0.0870 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 38 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 GLN B 197 ASN ** 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: 0.8215 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6607 Z= 0.165 Angle : 0.465 7.699 8946 Z= 0.243 Chirality : 0.039 0.138 1009 Planarity : 0.004 0.045 1134 Dihedral : 3.870 17.015 873 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.25 % Allowed : 18.45 % Favored : 80.31 % 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: 1.61 (0.29), residues: 785 helix: 2.37 (0.28), residues: 333 sheet: 0.09 (0.48), residues: 115 loop : 0.18 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.016 0.002 PHE A 253 TYR 0.013 0.001 TYR B 482 ARG 0.006 0.000 ARG B 541 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 96 time to evaluate : 0.697 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 104 average time/residue: 1.6126 time to fit residues: 175.2909 Evaluate side-chains 105 residues out of total 724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 97 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.2464 time to fit residues: 1.4967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 64 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.0170 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 ASN A 366 GLN ** B 569 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.140141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.110460 restraints weight = 10652.926| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.04 r_work: 0.3148 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6607 Z= 0.161 Angle : 0.462 7.596 8946 Z= 0.242 Chirality : 0.039 0.140 1009 Planarity : 0.004 0.048 1134 Dihedral : 3.885 16.777 873 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 1.53 % Allowed : 17.89 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.29), residues: 785 helix: 2.34 (0.28), residues: 333 sheet: 0.12 (0.48), residues: 115 loop : 0.18 (0.32), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 401 HIS 0.003 0.001 HIS A 328 PHE 0.016 0.002 PHE A 253 TYR 0.013 0.001 TYR B 482 ARG 0.007 0.000 ARG B 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3351.27 seconds wall clock time: 60 minutes 9.96 seconds (3609.96 seconds total)