Starting phenix.real_space_refine on Tue Feb 13 13:16:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr4_34045/02_2024/7yr4_34045.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr4_34045/02_2024/7yr4_34045.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr4_34045/02_2024/7yr4_34045.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr4_34045/02_2024/7yr4_34045.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr4_34045/02_2024/7yr4_34045.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yr4_34045/02_2024/7yr4_34045.pdb" } resolution = 4.12 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= 0.016 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 37 5.16 5 C 4103 2.51 5 N 1064 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 166": "OE1" <-> "OE2" Residue "A GLU 189": "OE1" <-> "OE2" Residue "A TYR 202": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 308": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 312": "OE1" <-> "OE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 350": "OD1" <-> "OD2" Residue "A ASP 367": "OD1" <-> "OD2" Residue "A ASP 368": "OD1" <-> "OD2" Residue "A TYR 385": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 427": "OD1" <-> "OD2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 495": "OE1" <-> "OE2" Residue "A PHE 504": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 549": "OE1" <-> "OE2" Residue "D GLU 340": "OE1" <-> "OE2" Residue "D TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6394 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 592, 4832 Classifications: {'peptide': 592} Link IDs: {'PTRANS': 26, 'TRANS': 565} Chain: "D" Number of atoms: 1562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1562 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 12, 'TRANS': 182} Time building chain proxies: 4.04, per 1000 atoms: 0.63 Number of scatterers: 6394 At special positions: 0 Unit cell: (84.24, 87.36, 118.56, 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 37 16.00 O 1190 8.00 N 1064 7.00 C 4103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 141 " distance=2.03 Simple disulfide: pdb=" SG CYS A 344 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 530 " - pdb=" SG CYS A 542 " distance=2.04 Simple disulfide: pdb=" SG CYS D 336 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 379 " - pdb=" SG CYS D 432 " distance=2.04 Simple disulfide: pdb=" SG CYS D 391 " - pdb=" SG CYS D 525 " distance=2.03 Simple disulfide: pdb=" SG CYS D 480 " - pdb=" SG CYS D 488 " distance=2.03 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: 2.32 Conformation dependent library (CDL) restraints added in 1.3 seconds 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1484 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 4 sheets defined 51.3% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 20 through 53 removed outlier: 3.726A pdb=" N GLU A 35 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLN A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 82 Processing helix chain 'A' and resid 92 through 101 Processing helix chain 'A' and resid 109 through 129 removed outlier: 3.594A pdb=" N SER A 113 " --> pdb=" O SER A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 155 removed outlier: 3.994A pdb=" N GLU A 150 " --> pdb=" O PRO A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 193 removed outlier: 3.665A pdb=" N ARG A 161 " --> pdb=" O ASP A 157 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLN A 175 " --> pdb=" O GLU A 171 " (cutoff:3.500A) Proline residue: A 178 - end of helix removed outlier: 4.003A pdb=" N VAL A 185 " --> pdb=" O GLU A 181 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N LEU A 186 " --> pdb=" O GLU A 182 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLU A 189 " --> pdb=" O VAL A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 196 No H-bonds generated for 'chain 'A' and resid 194 through 196' Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 219 through 252 Proline residue: A 235 - end of helix Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.683A pdb=" N LEU A 266 " --> pdb=" O PRO A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 283 Processing helix chain 'A' and resid 293 through 299 removed outlier: 3.650A pdb=" N MET A 297 " --> pdb=" O THR A 294 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N VAL A 298 " --> pdb=" O ASP A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 removed outlier: 3.564A pdb=" N ALA A 311 " --> pdb=" O ILE A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 331 removed outlier: 4.251A pdb=" N GLU A 329 " --> pdb=" O GLN A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 385 Processing helix chain 'A' and resid 386 through 388 No H-bonds generated for 'chain 'A' and resid 386 through 388' Processing helix chain 'A' and resid 400 through 412 removed outlier: 3.800A pdb=" N GLY A 405 " --> pdb=" O HIS A 401 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 406 " --> pdb=" O GLU A 402 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU A 410 " --> pdb=" O GLU A 406 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A 411 " --> pdb=" O ILE A 407 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA A 412 " --> pdb=" O MET A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 421 removed outlier: 3.663A pdb=" N LEU A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 447 removed outlier: 4.174A pdb=" N LYS A 441 " --> pdb=" O ASN A 437 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 442 " --> pdb=" O PHE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 466 removed outlier: 3.992A pdb=" N PHE A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 484 Processing helix chain 'A' and resid 499 through 502 Processing helix chain 'A' and resid 503 through 509 removed outlier: 4.076A pdb=" N SER A 507 " --> pdb=" O LEU A 503 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN A 508 " --> pdb=" O PHE A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 530 removed outlier: 3.591A pdb=" N TYR A 516 " --> pdb=" O PHE A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 559 Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 581 through 600 Proline residue: A 590 - end of helix removed outlier: 4.403A pdb=" N TRP A 594 " --> pdb=" O PRO A 590 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N LYS A 596 " --> pdb=" O PHE A 592 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N ASP A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 342 removed outlier: 3.624A pdb=" N VAL D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 366 through 371 Processing helix chain 'D' and resid 405 through 407 No H-bonds generated for 'chain 'D' and resid 405 through 407' Processing sheet with id=AA1, first strand: chain 'A' and resid 347 through 350 Processing sheet with id=AA2, first strand: chain 'D' and resid 356 through 358 Processing sheet with id=AA3, first strand: chain 'D' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'D' and resid 473 through 474 removed outlier: 3.551A pdb=" N TYR D 473 " --> pdb=" O TYR D 489 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N TYR D 489 " --> pdb=" O TYR D 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 272 hydrogen bonds defined for protein. 795 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: 1.65 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.09 - 1.23: 406 1.23 - 1.38: 2252 1.38 - 1.53: 3633 1.53 - 1.68: 229 1.68 - 1.83: 58 Bond restraints: 6578 Sorted by residual: bond pdb=" CG PRO D 373 " pdb=" CD PRO D 373 " ideal model delta sigma weight residual 1.503 1.085 0.418 3.40e-02 8.65e+02 1.51e+02 bond pdb=" CB PRO D 373 " pdb=" CG PRO D 373 " ideal model delta sigma weight residual 1.492 1.217 0.275 5.00e-02 4.00e+02 3.03e+01 bond pdb=" N PRO D 373 " pdb=" CD PRO D 373 " ideal model delta sigma weight residual 1.473 1.517 -0.044 1.40e-02 5.10e+03 9.86e+00 bond pdb=" CB ASN A 601 " pdb=" CG ASN A 601 " ideal model delta sigma weight residual 1.516 1.562 -0.046 2.50e-02 1.60e+03 3.36e+00 bond pdb=" CG LYS D 478 " pdb=" CD LYS D 478 " ideal model delta sigma weight residual 1.520 1.572 -0.052 3.00e-02 1.11e+03 3.06e+00 ... (remaining 6573 not shown) Histogram of bond angle deviations from ideal: 75.60 - 89.88: 2 89.88 - 104.16: 106 104.16 - 118.44: 4867 118.44 - 132.72: 3939 132.72 - 147.00: 24 Bond angle restraints: 8938 Sorted by residual: angle pdb=" N PRO D 373 " pdb=" CD PRO D 373 " pdb=" CG PRO D 373 " ideal model delta sigma weight residual 103.20 75.60 27.60 1.50e+00 4.44e-01 3.39e+02 angle pdb=" CB PRO D 373 " pdb=" CG PRO D 373 " pdb=" CD PRO D 373 " ideal model delta sigma weight residual 106.10 147.00 -40.90 3.20e+00 9.77e-02 1.63e+02 angle pdb=" CA PRO D 373 " pdb=" CB PRO D 373 " pdb=" CG PRO D 373 " ideal model delta sigma weight residual 104.50 80.22 24.28 1.90e+00 2.77e-01 1.63e+02 angle pdb=" CA PRO D 373 " pdb=" N PRO D 373 " pdb=" CD PRO D 373 " ideal model delta sigma weight residual 112.00 103.00 9.00 1.40e+00 5.10e-01 4.13e+01 angle pdb=" C LYS A 600 " pdb=" N ASN A 601 " pdb=" CA ASN A 601 " ideal model delta sigma weight residual 123.05 130.49 -7.44 1.57e+00 4.06e-01 2.25e+01 ... (remaining 8933 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 3445 17.77 - 35.55: 354 35.55 - 53.32: 58 53.32 - 71.09: 15 71.09 - 88.86: 10 Dihedral angle restraints: 3882 sinusoidal: 1571 harmonic: 2311 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 141 " pdb=" CB CYS A 141 " ideal model delta sinusoidal sigma weight residual 93.00 19.27 73.73 1 1.00e+01 1.00e-02 6.91e+01 dihedral pdb=" CB CYS D 336 " pdb=" SG CYS D 336 " pdb=" SG CYS D 361 " pdb=" CB CYS D 361 " ideal model delta sinusoidal sigma weight residual 93.00 19.50 73.50 1 1.00e+01 1.00e-02 6.87e+01 dihedral pdb=" CB CYS D 391 " pdb=" SG CYS D 391 " pdb=" SG CYS D 525 " pdb=" CB CYS D 525 " ideal model delta sinusoidal sigma weight residual -86.00 -146.07 60.07 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 3879 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 741 0.063 - 0.126: 159 0.126 - 0.189: 28 0.189 - 0.252: 2 0.252 - 0.315: 1 Chirality restraints: 931 Sorted by residual: chirality pdb=" CB VAL A 293 " pdb=" CA VAL A 293 " pdb=" CG1 VAL A 293 " pdb=" CG2 VAL A 293 " both_signs ideal model delta sigma weight residual False -2.63 -2.31 -0.32 2.00e-01 2.50e+01 2.49e+00 chirality pdb=" CA ASN A 601 " pdb=" N ASN A 601 " pdb=" C ASN A 601 " pdb=" CB ASN A 601 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL A 364 " pdb=" CA VAL A 364 " pdb=" CG1 VAL A 364 " pdb=" CG2 VAL A 364 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 ... (remaining 928 not shown) Planarity restraints: 1159 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 477 " 0.031 2.00e-02 2.50e+03 3.06e-02 2.35e+01 pdb=" CG TRP A 477 " -0.082 2.00e-02 2.50e+03 pdb=" CD1 TRP A 477 " 0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP A 477 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 477 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 477 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP A 477 " 0.007 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 477 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 477 " 0.007 2.00e-02 2.50e+03 pdb=" CH2 TRP A 477 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 288 " 0.062 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO A 289 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO A 289 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO A 289 " 0.051 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 459 " -0.017 2.00e-02 2.50e+03 2.25e-02 1.26e+01 pdb=" CG TRP A 459 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 459 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP A 459 " -0.013 2.00e-02 2.50e+03 pdb=" NE1 TRP A 459 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 459 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 459 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 459 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 459 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 459 " 0.002 2.00e-02 2.50e+03 ... (remaining 1156 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 961 2.76 - 3.29: 6316 3.29 - 3.83: 10623 3.83 - 4.36: 12003 4.36 - 4.90: 19898 Nonbonded interactions: 49801 Sorted by model distance: nonbonded pdb=" O LEU A 278 " pdb=" OG1 THR A 282 " model vdw 2.224 2.440 nonbonded pdb=" OH TYR A 83 " pdb=" OH TYR D 489 " model vdw 2.294 2.440 nonbonded pdb=" O SER A 105 " pdb=" OG SER A 113 " model vdw 2.309 2.440 nonbonded pdb=" O HIS A 239 " pdb=" ND2 ASN A 599 " model vdw 2.313 2.520 nonbonded pdb=" O THR D 393 " pdb=" OG1 THR D 523 " model vdw 2.322 2.440 ... (remaining 49796 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 7.120 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 21.120 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5610 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 : 0.008 0.418 6578 Z= 0.427 Angle : 1.165 40.904 8938 Z= 0.599 Chirality : 0.055 0.315 931 Planarity : 0.007 0.095 1159 Dihedral : 14.906 88.862 2377 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.63 % Twisted General : 0.40 % 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: -1.79 (0.27), residues: 783 helix: -0.62 (0.25), residues: 350 sheet: -1.30 (0.76), residues: 32 loop : -1.68 (0.28), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.004 TRP A 477 HIS 0.005 0.001 HIS D 519 PHE 0.035 0.003 PHE D 497 TYR 0.030 0.003 TYR A 279 ARG 0.006 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 270 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 410 LEU cc_start: 0.7503 (mt) cc_final: 0.6836 (mt) REVERT: A 520 LEU cc_start: 0.6720 (mp) cc_final: 0.6272 (tt) REVERT: A 523 PHE cc_start: 0.6854 (m-80) cc_final: 0.6493 (m-80) REVERT: A 543 ASP cc_start: 0.4915 (t0) cc_final: 0.4563 (t0) REVERT: A 587 TYR cc_start: 0.5147 (t80) cc_final: 0.4703 (t80) REVERT: A 592 PHE cc_start: 0.4417 (t80) cc_final: 0.3218 (t80) outliers start: 0 outliers final: 0 residues processed: 270 average time/residue: 0.2209 time to fit residues: 74.5506 Evaluate side-chains 150 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 32 optimal weight: 7.9990 chunk 20 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 37 optimal weight: 8.9990 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.8980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 58 ASN ** A 505 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6578 Z= 0.229 Angle : 0.689 12.343 8938 Z= 0.354 Chirality : 0.043 0.150 931 Planarity : 0.006 0.064 1159 Dihedral : 5.696 31.104 854 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -1.02 (0.28), residues: 783 helix: 0.15 (0.27), residues: 361 sheet: -0.84 (0.76), residues: 33 loop : -1.47 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 459 HIS 0.010 0.002 HIS A 345 PHE 0.016 0.002 PHE A 525 TYR 0.023 0.002 TYR A 385 ARG 0.006 0.001 ARG D 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 SER cc_start: 0.7007 (m) cc_final: 0.6747 (p) REVERT: A 216 ASP cc_start: 0.5550 (m-30) cc_final: 0.5244 (m-30) REVERT: A 380 GLN cc_start: 0.7110 (tp40) cc_final: 0.6736 (tp40) REVERT: A 408 MET cc_start: 0.7570 (mmm) cc_final: 0.7259 (mmm) REVERT: D 417 ASN cc_start: 0.7342 (p0) cc_final: 0.7034 (p0) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.2256 time to fit residues: 54.1474 Evaluate side-chains 143 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 19 optimal weight: 0.0270 chunk 70 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 56 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 GLN A 239 HIS ** A 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6107 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6578 Z= 0.174 Angle : 0.642 9.025 8938 Z= 0.329 Chirality : 0.042 0.147 931 Planarity : 0.005 0.049 1159 Dihedral : 5.200 28.353 854 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 17.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % 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: -0.73 (0.29), residues: 783 helix: 0.44 (0.28), residues: 359 sheet: -0.83 (0.77), residues: 33 loop : -1.34 (0.30), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 473 HIS 0.005 0.001 HIS A 265 PHE 0.017 0.001 PHE A 356 TYR 0.020 0.002 TYR D 495 ARG 0.007 0.001 ARG D 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 175 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 380 GLN cc_start: 0.7119 (tp40) cc_final: 0.6783 (tp40) REVERT: A 455 MET cc_start: 0.6731 (ppp) cc_final: 0.6398 (ppp) REVERT: A 587 TYR cc_start: 0.5889 (t80) cc_final: 0.5297 (t80) REVERT: D 417 ASN cc_start: 0.7506 (p0) cc_final: 0.7214 (p0) outliers start: 0 outliers final: 0 residues processed: 175 average time/residue: 0.2080 time to fit residues: 47.6413 Evaluate side-chains 135 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 67 optimal weight: 3.9990 chunk 20 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 58 ASN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS A 535 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6578 Z= 0.183 Angle : 0.627 7.207 8938 Z= 0.323 Chirality : 0.043 0.155 931 Planarity : 0.005 0.050 1159 Dihedral : 5.003 27.021 854 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -0.60 (0.29), residues: 783 helix: 0.45 (0.28), residues: 362 sheet: -0.59 (0.79), residues: 33 loop : -1.19 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP A 461 HIS 0.005 0.001 HIS A 265 PHE 0.017 0.001 PHE A 525 TYR 0.024 0.002 TYR A 515 ARG 0.005 0.001 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 165 time to evaluate : 0.797 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 216 ASP cc_start: 0.5726 (m-30) cc_final: 0.5524 (m-30) REVERT: A 455 MET cc_start: 0.6851 (ppp) cc_final: 0.5976 (ppp) REVERT: A 587 TYR cc_start: 0.6006 (t80) cc_final: 0.5451 (t80) outliers start: 0 outliers final: 0 residues processed: 165 average time/residue: 0.1884 time to fit residues: 40.8737 Evaluate side-chains 132 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 chunk 31 optimal weight: 8.9990 chunk 64 optimal weight: 0.0270 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 overall best weight: 0.7640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 345 HIS A 493 HIS A 535 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 599 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6139 moved from start: 0.5737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6578 Z= 0.150 Angle : 0.604 6.670 8938 Z= 0.308 Chirality : 0.043 0.155 931 Planarity : 0.004 0.043 1159 Dihedral : 4.863 24.775 854 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % 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: -0.49 (0.30), residues: 783 helix: 0.51 (0.27), residues: 363 sheet: -0.51 (0.78), residues: 34 loop : -1.10 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP A 461 HIS 0.006 0.001 HIS A 265 PHE 0.020 0.002 PHE A 592 TYR 0.017 0.001 TYR D 495 ARG 0.003 0.000 ARG A 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 455 MET cc_start: 0.6846 (ppp) cc_final: 0.5582 (ppp) REVERT: A 520 LEU cc_start: 0.6945 (tt) cc_final: 0.6735 (mt) REVERT: A 587 TYR cc_start: 0.5997 (t80) cc_final: 0.5420 (t80) REVERT: D 417 ASN cc_start: 0.7262 (p0) cc_final: 0.6962 (p0) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.1840 time to fit residues: 39.5585 Evaluate side-chains 131 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 8 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN A 61 ASN A 90 ASN A 121 ASN A 330 ASN A 535 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 339 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6577 moved from start: 0.7098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 6578 Z= 0.351 Angle : 0.815 13.219 8938 Z= 0.432 Chirality : 0.047 0.171 931 Planarity : 0.006 0.065 1159 Dihedral : 5.829 27.877 854 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 31.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % 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: -1.16 (0.28), residues: 783 helix: -0.07 (0.26), residues: 383 sheet: -0.79 (0.77), residues: 34 loop : -1.49 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.003 TRP A 473 HIS 0.013 0.003 HIS A 241 PHE 0.026 0.002 PHE A 274 TYR 0.023 0.003 TYR A 202 ARG 0.008 0.001 ARG D 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.6866 (mt) cc_final: 0.6618 (mt) REVERT: A 523 PHE cc_start: 0.6833 (m-80) cc_final: 0.6533 (m-80) REVERT: A 587 TYR cc_start: 0.6468 (t80) cc_final: 0.5641 (t80) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2132 time to fit residues: 47.6209 Evaluate side-chains 133 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.0170 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 0.0010 chunk 75 optimal weight: 0.7980 chunk 47 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 44 optimal weight: 0.0770 chunk 22 optimal weight: 0.9990 overall best weight: 0.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 90 ASN A 330 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 535 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 ASN ** D 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6327 moved from start: 0.7141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 6578 Z= 0.195 Angle : 0.694 9.306 8938 Z= 0.359 Chirality : 0.047 0.173 931 Planarity : 0.004 0.039 1159 Dihedral : 5.381 23.491 854 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 20.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % 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: -0.63 (0.29), residues: 783 helix: 0.43 (0.27), residues: 371 sheet: -0.03 (0.77), residues: 32 loop : -1.32 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.068 0.003 TRP A 461 HIS 0.007 0.001 HIS A 265 PHE 0.034 0.002 PHE A 356 TYR 0.018 0.002 TYR A 521 ARG 0.009 0.001 ARG A 306 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.826 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8925 (ppp) cc_final: 0.8359 (ppp) REVERT: A 455 MET cc_start: 0.6953 (ppp) cc_final: 0.6245 (ppp) REVERT: A 587 TYR cc_start: 0.5846 (t80) cc_final: 0.5217 (t80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.2161 time to fit residues: 45.7566 Evaluate side-chains 136 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.9990 chunk 47 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 72 optimal weight: 0.0770 chunk 65 optimal weight: 9.9990 chunk 70 optimal weight: 8.9990 chunk 42 optimal weight: 0.4980 overall best weight: 0.6940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 535 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 370 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6308 moved from start: 0.7305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6578 Z= 0.173 Angle : 0.696 9.053 8938 Z= 0.360 Chirality : 0.047 0.193 931 Planarity : 0.004 0.038 1159 Dihedral : 5.244 23.533 854 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: -0.59 (0.29), residues: 783 helix: 0.50 (0.27), residues: 369 sheet: 0.17 (0.76), residues: 32 loop : -1.34 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.003 TRP A 163 HIS 0.007 0.001 HIS A 241 PHE 0.028 0.002 PHE A 356 TYR 0.041 0.002 TYR A 521 ARG 0.018 0.001 ARG A 204 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.781 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 207 TYR cc_start: 0.5806 (m-80) cc_final: 0.5481 (m-80) REVERT: A 455 MET cc_start: 0.6805 (ppp) cc_final: 0.5667 (ppp) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.1862 time to fit residues: 40.3151 Evaluate side-chains 136 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 0.0770 chunk 66 optimal weight: 9.9990 chunk 69 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 35 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 overall best weight: 1.5944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS A 535 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6372 moved from start: 0.7557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 6578 Z= 0.195 Angle : 0.705 11.768 8938 Z= 0.360 Chirality : 0.046 0.179 931 Planarity : 0.004 0.037 1159 Dihedral : 5.284 22.797 854 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 21.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: -0.70 (0.29), residues: 783 helix: 0.34 (0.27), residues: 376 sheet: 0.15 (0.75), residues: 32 loop : -1.34 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.003 TRP A 461 HIS 0.007 0.001 HIS A 241 PHE 0.027 0.002 PHE A 464 TYR 0.015 0.002 TYR D 495 ARG 0.009 0.001 ARG A 177 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8975 (ppp) cc_final: 0.8339 (ppp) REVERT: A 154 ASN cc_start: 0.8043 (m110) cc_final: 0.7839 (m110) outliers start: 0 outliers final: 0 residues processed: 155 average time/residue: 0.1821 time to fit residues: 37.8155 Evaluate side-chains 131 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 0.3980 chunk 37 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 300 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 535 HIS ** A 556 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.7710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 6578 Z= 0.179 Angle : 0.711 12.955 8938 Z= 0.360 Chirality : 0.046 0.155 931 Planarity : 0.004 0.038 1159 Dihedral : 5.205 21.805 854 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 19.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.68 (0.29), residues: 783 helix: 0.25 (0.27), residues: 376 sheet: 0.22 (0.76), residues: 32 loop : -1.21 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP A 461 HIS 0.008 0.002 HIS A 265 PHE 0.026 0.002 PHE A 464 TYR 0.019 0.001 TYR A 516 ARG 0.006 0.001 ARG A 177 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1566 Ramachandran restraints generated. 783 Oldfield, 0 Emsley, 783 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 MET cc_start: 0.8959 (ppp) cc_final: 0.8370 (ppp) outliers start: 0 outliers final: 0 residues processed: 158 average time/residue: 0.1713 time to fit residues: 36.1605 Evaluate side-chains 129 residues out of total 691 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 chunk 25 optimal weight: 7.9990 chunk 63 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.1980 chunk 54 optimal weight: 0.2980 chunk 3 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 0.0040 chunk 41 optimal weight: 4.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 58 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 388 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 556 ASN ** 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 = 0.3724 r_free = 0.3724 target = 0.082372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.065706 restraints weight = 28617.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.068054 restraints weight = 19814.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.069840 restraints weight = 14862.799| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.7855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6578 Z= 0.179 Angle : 0.724 10.869 8938 Z= 0.369 Chirality : 0.046 0.238 931 Planarity : 0.005 0.039 1159 Dihedral : 5.173 21.646 854 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % 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: -0.63 (0.30), residues: 783 helix: 0.30 (0.27), residues: 377 sheet: 0.19 (0.74), residues: 32 loop : -1.20 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP A 461 HIS 0.007 0.001 HIS A 265 PHE 0.024 0.002 PHE A 464 TYR 0.019 0.001 TYR A 516 ARG 0.009 0.001 ARG A 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1926.45 seconds wall clock time: 35 minutes 34.60 seconds (2134.60 seconds total)