Starting phenix.real_space_refine on Mon Sep 23 19:48:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/09_2024/7k1v_22630.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/09_2024/7k1v_22630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/09_2024/7k1v_22630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/09_2024/7k1v_22630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/09_2024/7k1v_22630.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7k1v_22630/09_2024/7k1v_22630.cif" } resolution = 4.6 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= 1.000 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 9 5.16 5 C 3138 2.51 5 N 888 2.21 5 O 936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4971 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 626, 4971 Classifications: {'peptide': 626} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 599} Chain breaks: 3 Time building chain proxies: 3.55, per 1000 atoms: 0.71 Number of scatterers: 4971 At special positions: 0 Unit cell: (90.355, 76.536, 91.418, 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 9 16.00 O 936 8.00 N 888 7.00 C 3138 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 - 3.00 Amino acid : True - 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: 1.08 Conformation dependent library (CDL) restraints added in 571.8 milliseconds 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 3 sheets defined 60.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.76 Creating SS restraints... Processing helix chain 'A' and resid 19 through 28 removed outlier: 8.375A pdb=" N PHE A 25 " --> pdb=" O GLN A 21 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLY A 26 " --> pdb=" O ASP A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 36 removed outlier: 3.759A pdb=" N LEU A 33 " --> pdb=" O ASN A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 69 removed outlier: 3.678A pdb=" N GLN A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL A 59 " --> pdb=" O ALA A 55 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ARG A 60 " --> pdb=" O GLU A 56 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N ASP A 61 " --> pdb=" O THR A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 removed outlier: 3.745A pdb=" N ASP A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 95 removed outlier: 3.606A pdb=" N ARG A 95 " --> pdb=" O GLU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.587A pdb=" N LEU A 101 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE A 108 " --> pdb=" O GLU A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 127 removed outlier: 3.895A pdb=" N THR A 123 " --> pdb=" O ALA A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 removed outlier: 4.448A pdb=" N ARG A 165 " --> pdb=" O GLU A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 174 Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 193 through 210 removed outlier: 4.040A pdb=" N VAL A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA A 204 " --> pdb=" O ASP A 200 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LEU A 205 " --> pdb=" O ARG A 201 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N GLU A 206 " --> pdb=" O ILE A 202 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N THR A 207 " --> pdb=" O VAL A 203 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N LYS A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 221 removed outlier: 3.667A pdb=" N ARG A 219 " --> pdb=" O ASP A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 238 Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 267 through 278 Processing helix chain 'A' and resid 279 through 295 removed outlier: 3.988A pdb=" N CYS A 285 " --> pdb=" O GLU A 281 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N TRP A 286 " --> pdb=" O ASP A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 303 through 312 removed outlier: 3.706A pdb=" N ASP A 307 " --> pdb=" O LEU A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 328 Processing helix chain 'A' and resid 328 through 336 removed outlier: 4.122A pdb=" N VAL A 332 " --> pdb=" O GLY A 328 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N GLU A 333 " --> pdb=" O VAL A 329 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN A 334 " --> pdb=" O SER A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 349 Processing helix chain 'A' and resid 352 through 372 removed outlier: 4.081A pdb=" N ARG A 356 " --> pdb=" O ASP A 352 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N ASP A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N ASN A 363 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLU A 366 " --> pdb=" O ASP A 362 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ARG A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 370 " --> pdb=" O GLU A 366 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE A 372 " --> pdb=" O TYR A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 379 through 389 removed outlier: 4.164A pdb=" N ARG A 385 " --> pdb=" O GLN A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 437 removed outlier: 3.719A pdb=" N VAL A 426 " --> pdb=" O ARG A 422 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN A 427 " --> pdb=" O GLY A 423 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ASP A 429 " --> pdb=" O ALA A 425 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLU A 431 " --> pdb=" O ASN A 427 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 433 " --> pdb=" O ASP A 429 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 434 " --> pdb=" O ARG A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 479 through 499 removed outlier: 3.787A pdb=" N ASN A 483 " --> pdb=" O ASP A 479 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N ILE A 487 " --> pdb=" O ASN A 483 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ALA A 489 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 500 through 506 Processing helix chain 'A' and resid 517 through 528 removed outlier: 3.662A pdb=" N ARG A 521 " --> pdb=" O THR A 517 " (cutoff:3.500A) Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 535 through 537 No H-bonds generated for 'chain 'A' and resid 535 through 537' Processing helix chain 'A' and resid 558 through 572 removed outlier: 4.592A pdb=" N GLY A 563 " --> pdb=" O GLY A 559 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ASP A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU A 565 " --> pdb=" O ASN A 561 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ILE A 570 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU A 572 " --> pdb=" O LEU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 580 Processing helix chain 'A' and resid 591 through 602 removed outlier: 3.529A pdb=" N TRP A 600 " --> pdb=" O VAL A 596 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLN A 602 " --> pdb=" O PHE A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 610 through 616 Processing helix chain 'A' and resid 617 through 620 removed outlier: 3.866A pdb=" N ASP A 620 " --> pdb=" O LEU A 617 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 617 through 620' Processing helix chain 'A' and resid 624 through 629 removed outlier: 3.823A pdb=" N ARG A 628 " --> pdb=" O PRO A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.707A pdb=" N ARG A 634 " --> pdb=" O GLY A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 644 Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 45 Processing sheet with id=AA2, first strand: chain 'A' and resid 150 through 151 Processing sheet with id=AA3, first strand: chain 'A' and resid 454 through 455 removed outlier: 3.757A pdb=" N TYR A 454 " --> pdb=" O VAL A 463 " (cutoff:3.500A) 183 hydrogen bonds defined for protein. 531 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: 1.17 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1509 1.34 - 1.45: 969 1.45 - 1.57: 2598 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 5092 Sorted by residual: bond pdb=" N VAL A 397 " pdb=" CA VAL A 397 " ideal model delta sigma weight residual 1.456 1.495 -0.040 1.11e-02 8.12e+03 1.27e+01 bond pdb=" N VAL A 543 " pdb=" CA VAL A 543 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.17e-02 7.31e+03 8.99e+00 bond pdb=" N ARG A 146 " pdb=" CA ARG A 146 " ideal model delta sigma weight residual 1.457 1.496 -0.038 1.29e-02 6.01e+03 8.90e+00 bond pdb=" N ILE A 156 " pdb=" CA ILE A 156 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.10e-02 8.26e+03 8.69e+00 bond pdb=" N TYR A 538 " pdb=" CA TYR A 538 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.18e-02 7.18e+03 8.23e+00 ... (remaining 5087 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 6329 1.89 - 3.77: 510 3.77 - 5.66: 75 5.66 - 7.54: 12 7.54 - 9.43: 2 Bond angle restraints: 6928 Sorted by residual: angle pdb=" N ARG A 126 " pdb=" CA ARG A 126 " pdb=" C ARG A 126 " ideal model delta sigma weight residual 111.36 104.92 6.44 1.09e+00 8.42e-01 3.49e+01 angle pdb=" CA GLY A 398 " pdb=" C GLY A 398 " pdb=" O GLY A 398 " ideal model delta sigma weight residual 122.24 117.27 4.97 8.70e-01 1.32e+00 3.27e+01 angle pdb=" C GLU A 443 " pdb=" N TRP A 444 " pdb=" CA TRP A 444 " ideal model delta sigma weight residual 122.85 115.45 7.40 1.39e+00 5.18e-01 2.83e+01 angle pdb=" N ARG A 385 " pdb=" CA ARG A 385 " pdb=" C ARG A 385 " ideal model delta sigma weight residual 111.36 106.11 5.25 1.09e+00 8.42e-01 2.32e+01 angle pdb=" N ARG A 527 " pdb=" CA ARG A 527 " pdb=" C ARG A 527 " ideal model delta sigma weight residual 111.40 106.09 5.31 1.22e+00 6.72e-01 1.90e+01 ... (remaining 6923 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 2585 17.19 - 34.39: 320 34.39 - 51.58: 63 51.58 - 68.77: 13 68.77 - 85.97: 4 Dihedral angle restraints: 2985 sinusoidal: 1180 harmonic: 1805 Sorted by residual: dihedral pdb=" CA VAL A 28 " pdb=" C VAL A 28 " pdb=" N ASN A 29 " pdb=" CA ASN A 29 " ideal model delta harmonic sigma weight residual -180.00 -151.64 -28.36 0 5.00e+00 4.00e-02 3.22e+01 dihedral pdb=" CA LEU A 390 " pdb=" C LEU A 390 " pdb=" N ASN A 391 " pdb=" CA ASN A 391 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA ALA A 127 " pdb=" C ALA A 127 " pdb=" N GLY A 128 " pdb=" CA GLY A 128 " ideal model delta harmonic sigma weight residual 180.00 152.19 27.81 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 2982 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 542 0.056 - 0.111: 157 0.111 - 0.167: 30 0.167 - 0.222: 5 0.222 - 0.278: 2 Chirality restraints: 736 Sorted by residual: chirality pdb=" CA ARG A 126 " pdb=" N ARG A 126 " pdb=" C ARG A 126 " pdb=" CB ARG A 126 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA LYS A 396 " pdb=" N LYS A 396 " pdb=" C LYS A 396 " pdb=" CB LYS A 396 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA LEU A 158 " pdb=" N LEU A 158 " pdb=" C LEU A 158 " pdb=" CB LEU A 158 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 733 not shown) Planarity restraints: 920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 145 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C THR A 145 " -0.051 2.00e-02 2.50e+03 pdb=" O THR A 145 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG A 146 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 321 " 0.012 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C LEU A 321 " -0.044 2.00e-02 2.50e+03 pdb=" O LEU A 321 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG A 322 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP A 620 " -0.037 5.00e-02 4.00e+02 5.50e-02 4.84e+00 pdb=" N PRO A 621 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 621 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 621 " -0.031 5.00e-02 4.00e+02 ... (remaining 917 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 204 2.71 - 3.26: 5699 3.26 - 3.80: 8722 3.80 - 4.35: 11468 4.35 - 4.90: 16634 Nonbonded interactions: 42727 Sorted by model distance: nonbonded pdb=" O ASP A 140 " pdb=" OD1 ASP A 140 " model vdw 2.159 3.040 nonbonded pdb=" O ARG A 327 " pdb=" OG SER A 330 " model vdw 2.208 3.040 nonbonded pdb=" O GLY A 566 " pdb=" OG SER A 569 " model vdw 2.235 3.040 nonbonded pdb=" NE2 GLN A 365 " pdb=" O LEU A 390 " model vdw 2.237 3.120 nonbonded pdb=" OE1 GLN A 65 " pdb=" NH1 ARG A 347 " model vdw 2.259 3.120 ... (remaining 42722 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: 0.600 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.670 Find NCS groups from input model: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 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 0.062 5092 Z= 0.488 Angle : 1.116 9.430 6928 Z= 0.666 Chirality : 0.055 0.278 736 Planarity : 0.006 0.055 920 Dihedral : 15.771 85.967 1825 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 0.40 % Allowed : 6.39 % Favored : 93.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.04 (0.29), residues: 618 helix: -3.36 (0.23), residues: 209 sheet: -5.41 (0.56), residues: 10 loop : -2.32 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP A 32 HIS 0.008 0.002 HIS A 536 PHE 0.027 0.003 PHE A 652 TYR 0.032 0.003 TYR A 484 ARG 0.008 0.001 ARG A 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 111 time to evaluate : 0.517 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: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.8279 (m-80) cc_final: 0.7755 (m-10) REVERT: A 266 ASP cc_start: 0.8907 (m-30) cc_final: 0.8125 (t0) REVERT: A 293 ARG cc_start: 0.8677 (ttt-90) cc_final: 0.8169 (tpp80) REVERT: A 366 GLU cc_start: 0.8541 (tp30) cc_final: 0.7928 (tm-30) REVERT: A 397 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7924 (p) REVERT: A 431 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8107 (pp20) REVERT: A 462 ILE cc_start: 0.7452 (pt) cc_final: 0.7099 (pt) REVERT: A 480 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8852 (tm-30) REVERT: A 484 TYR cc_start: 0.8344 (t80) cc_final: 0.7779 (t80) REVERT: A 543 VAL cc_start: 0.1595 (OUTLIER) cc_final: 0.1339 (m) outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.2603 time to fit residues: 34.6027 Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 78 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 18 optimal weight: 0.0870 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 150 HIS A 227 ASN A 346 GLN A 365 GLN A 493 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6988 moved from start: 0.3288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5092 Z= 0.194 Angle : 0.687 8.207 6928 Z= 0.362 Chirality : 0.044 0.137 736 Planarity : 0.005 0.049 920 Dihedral : 6.736 26.982 696 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -3.65 (0.30), residues: 618 helix: -2.53 (0.23), residues: 314 sheet: -3.86 (1.50), residues: 10 loop : -2.14 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 298 HIS 0.007 0.001 HIS A 493 PHE 0.015 0.002 PHE A 652 TYR 0.009 0.001 TYR A 454 ARG 0.012 0.001 ARG A 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 0.530 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 231 PHE cc_start: 0.8289 (m-80) cc_final: 0.8049 (m-10) REVERT: A 266 ASP cc_start: 0.8717 (m-30) cc_final: 0.8256 (t0) REVERT: A 293 ARG cc_start: 0.8508 (ttt-90) cc_final: 0.8304 (tpp80) REVERT: A 462 ILE cc_start: 0.7005 (pt) cc_final: 0.6786 (pt) REVERT: A 534 GLN cc_start: 0.8048 (mt0) cc_final: 0.7659 (mp10) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2487 time to fit residues: 27.6121 Evaluate side-chains 65 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 50 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 45 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 5092 Z= 0.334 Angle : 0.738 10.523 6928 Z= 0.402 Chirality : 0.045 0.131 736 Planarity : 0.006 0.051 920 Dihedral : 6.827 29.746 696 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 29.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.20 % Allowed : 7.58 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -3.16 (0.31), residues: 618 helix: -2.13 (0.24), residues: 312 sheet: -3.46 (1.67), residues: 10 loop : -1.91 (0.38), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP A 286 HIS 0.008 0.002 HIS A 428 PHE 0.028 0.003 PHE A 445 TYR 0.025 0.003 TYR A 575 ARG 0.006 0.001 ARG A 527 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 86 time to evaluate : 0.490 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: symmetry clash REVERT: A 231 PHE cc_start: 0.8273 (m-80) cc_final: 0.7856 (m-10) REVERT: A 257 MET cc_start: -0.1519 (mtt) cc_final: -0.2995 (mtt) REVERT: A 266 ASP cc_start: 0.8863 (m-30) cc_final: 0.8386 (t0) outliers start: 1 outliers final: 0 residues processed: 86 average time/residue: 0.2300 time to fit residues: 24.4470 Evaluate side-chains 69 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 6 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 59 optimal weight: 7.9990 chunk 53 optimal weight: 20.0000 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 GLN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS A 497 HIS A 502 GLN A 663 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5092 Z= 0.181 Angle : 0.655 8.065 6928 Z= 0.343 Chirality : 0.043 0.144 736 Planarity : 0.005 0.053 920 Dihedral : 6.172 26.981 696 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 0.40 % Allowed : 4.39 % Favored : 95.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.68 (0.33), residues: 618 helix: -1.77 (0.25), residues: 329 sheet: -2.70 (1.85), residues: 10 loop : -1.60 (0.40), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 286 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.002 PHE A 310 TYR 0.016 0.002 TYR A 368 ARG 0.007 0.001 ARG A 54 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 81 time to evaluate : 0.543 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: A 231 PHE cc_start: 0.7965 (m-80) cc_final: 0.7681 (m-10) REVERT: A 257 MET cc_start: -0.2238 (mtt) cc_final: -0.3136 (mtt) REVERT: A 266 ASP cc_start: 0.8742 (m-30) cc_final: 0.8307 (t0) REVERT: A 529 LYS cc_start: 0.9489 (tmtt) cc_final: 0.9252 (tmtt) REVERT: A 602 GLN cc_start: 0.9138 (mp10) cc_final: 0.8901 (mp10) outliers start: 2 outliers final: 0 residues processed: 81 average time/residue: 0.2171 time to fit residues: 21.9538 Evaluate side-chains 61 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 5.9990 chunk 0 optimal weight: 9.9990 chunk 44 optimal weight: 7.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.3980 chunk 41 optimal weight: 8.9990 chunk 30 optimal weight: 0.9990 chunk 53 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 GLN ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN A 663 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.5175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5092 Z= 0.234 Angle : 0.655 11.611 6928 Z= 0.342 Chirality : 0.043 0.182 736 Planarity : 0.005 0.044 920 Dihedral : 6.010 21.786 696 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 0.20 % Allowed : 1.60 % Favored : 98.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.41 (0.33), residues: 618 helix: -1.57 (0.26), residues: 324 sheet: -2.31 (1.77), residues: 10 loop : -1.47 (0.40), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 286 HIS 0.005 0.002 HIS A 428 PHE 0.014 0.002 PHE A 241 TYR 0.013 0.002 TYR A 164 ARG 0.003 0.001 ARG A 301 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 82 time to evaluate : 0.552 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 87 PHE cc_start: 0.5155 (t80) cc_final: 0.4930 (t80) REVERT: A 90 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7312 (mm-30) REVERT: A 231 PHE cc_start: 0.7960 (m-80) cc_final: 0.7584 (m-10) REVERT: A 257 MET cc_start: -0.1532 (mtt) cc_final: -0.2649 (mtt) REVERT: A 266 ASP cc_start: 0.8795 (m-30) cc_final: 0.8275 (t70) REVERT: A 582 ASN cc_start: 0.9373 (m-40) cc_final: 0.8696 (t0) outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.1955 time to fit residues: 20.1414 Evaluate side-chains 65 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 65 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 0.1980 chunk 14 optimal weight: 0.0370 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 10.0000 chunk 31 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 34 optimal weight: 9.9990 overall best weight: 0.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5092 Z= 0.163 Angle : 0.623 9.591 6928 Z= 0.322 Chirality : 0.043 0.158 736 Planarity : 0.005 0.042 920 Dihedral : 5.637 20.864 696 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -2.17 (0.33), residues: 618 helix: -1.38 (0.26), residues: 336 sheet: -1.47 (2.00), residues: 10 loop : -1.34 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 286 HIS 0.003 0.001 HIS A 213 PHE 0.013 0.001 PHE A 308 TYR 0.013 0.001 TYR A 484 ARG 0.012 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.570 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: A 183 MET cc_start: 0.4152 (tpp) cc_final: 0.3656 (tpt) REVERT: A 231 PHE cc_start: 0.7777 (m-80) cc_final: 0.7463 (m-10) REVERT: A 257 MET cc_start: -0.2787 (mtt) cc_final: -0.3343 (mtt) REVERT: A 266 ASP cc_start: 0.8656 (m-30) cc_final: 0.8259 (t70) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.1928 time to fit residues: 19.6751 Evaluate side-chains 62 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 0.0370 chunk 33 optimal weight: 9.9990 chunk 50 optimal weight: 0.0060 chunk 59 optimal weight: 10.0000 chunk 37 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 overall best weight: 0.8076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 456 ASN A 663 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.5856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5092 Z= 0.164 Angle : 0.604 8.651 6928 Z= 0.311 Chirality : 0.042 0.143 736 Planarity : 0.005 0.063 920 Dihedral : 5.305 20.061 696 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.20 % Allowed : 0.80 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.34), residues: 618 helix: -1.07 (0.27), residues: 333 sheet: -1.00 (2.09), residues: 10 loop : -1.26 (0.40), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 286 HIS 0.003 0.001 HIS A 213 PHE 0.014 0.001 PHE A 308 TYR 0.012 0.001 TYR A 484 ARG 0.006 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 81 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 183 MET cc_start: 0.4202 (tpp) cc_final: 0.3733 (tpt) REVERT: A 231 PHE cc_start: 0.7755 (m-80) cc_final: 0.7468 (m-10) REVERT: A 257 MET cc_start: -0.2867 (mtt) cc_final: -0.3171 (mtt) REVERT: A 266 ASP cc_start: 0.8677 (m-30) cc_final: 0.8213 (t0) REVERT: A 279 ASN cc_start: 0.8263 (m-40) cc_final: 0.8009 (m-40) outliers start: 1 outliers final: 0 residues processed: 81 average time/residue: 0.2074 time to fit residues: 21.6731 Evaluate side-chains 62 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 62 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 5 optimal weight: 0.8980 chunk 46 optimal weight: 10.0000 chunk 54 optimal weight: 7.9990 chunk 57 optimal weight: 0.9980 chunk 52 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 169 HIS A 319 GLN A 511 ASN A 561 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5092 Z= 0.180 Angle : 0.624 7.900 6928 Z= 0.318 Chirality : 0.043 0.145 736 Planarity : 0.004 0.043 920 Dihedral : 5.294 22.008 696 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 18.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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: -1.62 (0.34), residues: 618 helix: -0.96 (0.28), residues: 326 sheet: -0.63 (2.16), residues: 10 loop : -1.09 (0.40), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 286 HIS 0.004 0.001 HIS A 213 PHE 0.015 0.002 PHE A 308 TYR 0.012 0.001 TYR A 484 ARG 0.007 0.001 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 0.554 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 183 MET cc_start: 0.4522 (tpp) cc_final: 0.4132 (tpt) REVERT: A 231 PHE cc_start: 0.7882 (m-80) cc_final: 0.7526 (m-10) REVERT: A 257 MET cc_start: -0.2775 (mtt) cc_final: -0.3080 (mtt) REVERT: A 266 ASP cc_start: 0.8565 (m-30) cc_final: 0.8046 (t0) REVERT: A 270 THR cc_start: 0.9033 (m) cc_final: 0.8744 (m) REVERT: A 336 MET cc_start: 0.7166 (mmp) cc_final: 0.6758 (mmp) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.1927 time to fit residues: 18.5926 Evaluate side-chains 61 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 17 optimal weight: 0.5980 chunk 50 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5092 Z= 0.160 Angle : 0.640 12.202 6928 Z= 0.319 Chirality : 0.043 0.151 736 Planarity : 0.005 0.042 920 Dihedral : 5.172 20.781 696 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 15.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % 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 (0.34), residues: 618 helix: -0.97 (0.27), residues: 340 sheet: -0.57 (2.20), residues: 10 loop : -1.23 (0.40), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 286 HIS 0.003 0.001 HIS A 213 PHE 0.021 0.002 PHE A 598 TYR 0.015 0.001 TYR A 164 ARG 0.009 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 77 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 PHE cc_start: 0.7775 (m-80) cc_final: 0.7475 (m-10) REVERT: A 266 ASP cc_start: 0.8701 (m-30) cc_final: 0.8245 (t0) REVERT: A 336 MET cc_start: 0.7076 (mmp) cc_final: 0.6599 (mmp) REVERT: A 446 MET cc_start: 0.6991 (ppp) cc_final: 0.6787 (ppp) REVERT: A 447 THR cc_start: 0.8657 (m) cc_final: 0.8454 (m) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2002 time to fit residues: 19.4276 Evaluate side-chains 59 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 49 optimal weight: 0.8980 chunk 5 optimal weight: 0.0030 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 0.2980 chunk 39 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7037 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5092 Z= 0.168 Angle : 0.649 11.641 6928 Z= 0.327 Chirality : 0.044 0.226 736 Planarity : 0.005 0.042 920 Dihedral : 5.116 21.077 696 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.31 % Favored : 93.69 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.34), residues: 618 helix: -0.89 (0.27), residues: 341 sheet: -0.36 (2.25), residues: 10 loop : -1.25 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 286 HIS 0.004 0.001 HIS A 169 PHE 0.014 0.001 PHE A 308 TYR 0.010 0.001 TYR A 164 ARG 0.007 0.001 ARG A 413 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1236 Ramachandran restraints generated. 618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.511 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: A 231 PHE cc_start: 0.7808 (m-80) cc_final: 0.7582 (m-10) REVERT: A 266 ASP cc_start: 0.8731 (m-30) cc_final: 0.8207 (t0) REVERT: A 336 MET cc_start: 0.7132 (mmp) cc_final: 0.6730 (mmp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.2323 time to fit residues: 23.3866 Evaluate side-chains 63 residues out of total 501 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 63 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.2980 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 43 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.161412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.132242 restraints weight = 20514.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.133475 restraints weight = 18920.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.134187 restraints weight = 17666.523| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.6793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 5092 Z= 0.164 Angle : 0.640 11.348 6928 Z= 0.324 Chirality : 0.043 0.209 736 Planarity : 0.004 0.042 920 Dihedral : 5.011 20.369 696 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.20 % Allowed : 0.40 % Favored : 99.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.34), residues: 618 helix: -0.89 (0.27), residues: 346 sheet: -0.36 (2.24), residues: 10 loop : -1.28 (0.39), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 286 HIS 0.004 0.001 HIS A 213 PHE 0.011 0.001 PHE A 308 TYR 0.010 0.001 TYR A 484 ARG 0.006 0.001 ARG A 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1461.46 seconds wall clock time: 26 minutes 56.99 seconds (1616.99 seconds total)