Starting phenix.real_space_refine on Thu Mar 6 05:01:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k1v_22630/03_2025/7k1v_22630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k1v_22630/03_2025/7k1v_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/cci-nas-00/data/ceres_data/7k1v_22630/03_2025/7k1v_22630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k1v_22630/03_2025/7k1v_22630.map" model { file = "/net/cci-nas-00/data/ceres_data/7k1v_22630/03_2025/7k1v_22630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k1v_22630/03_2025/7k1v_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-5624/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: 3.42, per 1000 atoms: 0.69 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: 1.69 Conformation dependent library (CDL) restraints added in 800.2 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: 0.54 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: 1.31 Time building geometry restraints manager: 1.61 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: 0.400 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 16.610 Find NCS groups from input model: 0.060 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:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.470 ------------------------------------------------------------------------------- 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 to be fit. rotamer outliers: 2 poor density : 111 time to evaluate : 0.573 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: 0.2746 time to fit residues: 36.5882 Evaluate side-chains 80 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.156281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.123830 restraints weight = 18681.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.125198 restraints weight = 17190.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.125998 restraints weight = 16051.787| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 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 to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.516 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 214 TRP cc_start: 0.8562 (m-10) cc_final: 0.8299 (m-10) REVERT: A 231 PHE cc_start: 0.8494 (m-80) cc_final: 0.8141 (m-10) REVERT: A 266 ASP cc_start: 0.9195 (m-30) cc_final: 0.8681 (t0) REVERT: A 293 ARG cc_start: 0.9075 (ttt-90) cc_final: 0.8600 (tpp80) REVERT: A 431 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8709 (pp20) REVERT: A 462 ILE cc_start: 0.7190 (pt) cc_final: 0.6912 (pt) REVERT: A 514 ASP cc_start: 0.9120 (m-30) cc_final: 0.8916 (t0) REVERT: A 534 GLN cc_start: 0.8113 (mt0) cc_final: 0.7893 (mp10) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.2559 time to fit residues: 28.3170 Evaluate side-chains 67 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 45 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN ** A 493 HIS ** 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 = 0.4263 r_free = 0.4263 target = 0.147031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.116225 restraints weight = 19913.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.117001 restraints weight = 18532.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.118014 restraints weight = 17602.301| |-----------------------------------------------------------------------------| r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5092 Z= 0.235 Angle : 0.644 10.446 6928 Z= 0.346 Chirality : 0.043 0.137 736 Planarity : 0.005 0.045 920 Dihedral : 6.315 26.939 696 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.20 % Allowed : 5.59 % Favored : 94.21 % 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: -2.97 (0.32), residues: 618 helix: -2.00 (0.25), residues: 308 sheet: -3.54 (1.68), residues: 10 loop : -1.77 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 286 HIS 0.006 0.001 HIS A 428 PHE 0.017 0.002 PHE A 445 TYR 0.019 0.002 TYR A 484 ARG 0.005 0.001 ARG A 54 *********************** 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 91 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 90 time to evaluate : 0.960 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 214 TRP cc_start: 0.8780 (m-10) cc_final: 0.8250 (m-10) REVERT: A 231 PHE cc_start: 0.8247 (m-80) cc_final: 0.7829 (m-10) REVERT: A 257 MET cc_start: -0.0960 (mtt) cc_final: -0.2590 (mtt) REVERT: A 266 ASP cc_start: 0.9183 (m-30) cc_final: 0.8701 (t0) REVERT: A 293 ARG cc_start: 0.9149 (ttt-90) cc_final: 0.8714 (tpp80) REVERT: A 431 GLU cc_start: 0.8973 (mm-30) cc_final: 0.8620 (pp20) REVERT: A 462 ILE cc_start: 0.7298 (pt) cc_final: 0.6972 (pt) REVERT: A 604 TRP cc_start: 0.5414 (m100) cc_final: 0.5174 (m100) outliers start: 1 outliers final: 0 residues processed: 90 average time/residue: 0.2694 time to fit residues: 31.2509 Evaluate side-chains 66 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 4 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 0.0040 overall best weight: 1.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 233 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 561 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 663 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.148794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.117247 restraints weight = 19752.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.118618 restraints weight = 17952.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.119704 restraints weight = 16624.798| |-----------------------------------------------------------------------------| r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5092 Z= 0.205 Angle : 0.644 9.498 6928 Z= 0.338 Chirality : 0.044 0.155 736 Planarity : 0.005 0.043 920 Dihedral : 6.076 25.717 696 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.40 % Allowed : 4.59 % Favored : 95.01 % 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: -2.85 (0.32), residues: 618 helix: -1.81 (0.25), residues: 338 sheet: -3.14 (1.69), residues: 10 loop : -1.78 (0.39), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 286 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.002 PHE A 652 TYR 0.015 0.002 TYR A 368 ARG 0.004 0.000 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 86 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 84 time to evaluate : 0.518 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 214 TRP cc_start: 0.8538 (m-10) cc_final: 0.8217 (m-10) REVERT: A 231 PHE cc_start: 0.8222 (m-80) cc_final: 0.7760 (m-10) REVERT: A 257 MET cc_start: -0.0850 (mtt) cc_final: -0.2254 (mtt) REVERT: A 266 ASP cc_start: 0.9069 (m-30) cc_final: 0.8590 (t0) REVERT: A 293 ARG cc_start: 0.9093 (ttt-90) cc_final: 0.8660 (tpp80) REVERT: A 431 GLU cc_start: 0.8927 (mm-30) cc_final: 0.8619 (pp20) REVERT: A 462 ILE cc_start: 0.7265 (pt) cc_final: 0.6895 (pt) REVERT: A 470 GLN cc_start: 0.9666 (tt0) cc_final: 0.9446 (tt0) REVERT: A 582 ASN cc_start: 0.9477 (m110) cc_final: 0.9044 (t0) REVERT: A 602 GLN cc_start: 0.9297 (mp10) cc_final: 0.9036 (mp10) outliers start: 2 outliers final: 1 residues processed: 84 average time/residue: 0.1894 time to fit residues: 20.1401 Evaluate side-chains 66 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 47 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 233 GLN A 365 GLN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 HIS A 497 HIS A 502 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.152667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.120420 restraints weight = 19371.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.121735 restraints weight = 17787.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 16)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.122543 restraints weight = 16564.620| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5092 Z= 0.189 Angle : 0.618 11.496 6928 Z= 0.320 Chirality : 0.043 0.179 736 Planarity : 0.005 0.042 920 Dihedral : 5.758 24.393 696 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % 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: -2.35 (0.33), residues: 618 helix: -1.43 (0.27), residues: 322 sheet: -2.53 (1.80), residues: 10 loop : -1.56 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 286 HIS 0.006 0.001 HIS A 497 PHE 0.013 0.002 PHE A 310 TYR 0.012 0.002 TYR A 164 ARG 0.004 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 77 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.558 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 214 TRP cc_start: 0.8463 (m-10) cc_final: 0.8118 (m-10) REVERT: A 231 PHE cc_start: 0.8252 (m-80) cc_final: 0.7741 (m-10) REVERT: A 257 MET cc_start: -0.0877 (mtt) cc_final: -0.2157 (mtt) REVERT: A 266 ASP cc_start: 0.9119 (m-30) cc_final: 0.8567 (t0) REVERT: A 293 ARG cc_start: 0.9085 (ttt-90) cc_final: 0.8670 (tpp80) REVERT: A 431 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8677 (pp20) REVERT: A 582 ASN cc_start: 0.9486 (m110) cc_final: 0.9058 (t0) outliers start: 0 outliers final: 0 residues processed: 77 average time/residue: 0.2018 time to fit residues: 19.6947 Evaluate side-chains 61 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 18 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 40 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 8.9990 chunk 32 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.153085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.121768 restraints weight = 19418.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.122701 restraints weight = 17811.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.123913 restraints weight = 16755.049| |-----------------------------------------------------------------------------| r_work (final): 0.4051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.5377 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= 0.193 Angle : 0.610 9.430 6928 Z= 0.319 Chirality : 0.042 0.174 736 Planarity : 0.005 0.041 920 Dihedral : 5.608 20.964 696 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % 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: -2.07 (0.33), residues: 618 helix: -1.28 (0.27), residues: 322 sheet: -2.20 (1.78), residues: 10 loop : -1.31 (0.40), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 286 HIS 0.004 0.001 HIS A 213 PHE 0.014 0.002 PHE A 524 TYR 0.013 0.002 TYR A 164 ARG 0.005 0.001 ARG A 521 *********************** 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 76 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.668 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 231 PHE cc_start: 0.7905 (m-80) cc_final: 0.7520 (m-10) REVERT: A 257 MET cc_start: -0.1268 (mtt) cc_final: -0.2429 (mtt) REVERT: A 266 ASP cc_start: 0.8929 (m-30) cc_final: 0.8334 (t70) REVERT: A 293 ARG cc_start: 0.8987 (ttt-90) cc_final: 0.8682 (tpp80) REVERT: A 582 ASN cc_start: 0.9459 (m110) cc_final: 0.9003 (t0) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.2106 time to fit residues: 20.4850 Evaluate side-chains 61 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.0040 chunk 28 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 52 optimal weight: 0.2980 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 0.0170 chunk 9 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 overall best weight: 0.4430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 456 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.157592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.125801 restraints weight = 18087.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.127035 restraints weight = 16833.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.128164 restraints weight = 15433.879| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5831 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= 0.150 Angle : 0.603 8.519 6928 Z= 0.304 Chirality : 0.042 0.155 736 Planarity : 0.004 0.041 920 Dihedral : 5.162 19.251 696 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % 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: -1.85 (0.33), residues: 618 helix: -1.09 (0.27), residues: 336 sheet: -2.15 (1.78), residues: 10 loop : -1.20 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 286 HIS 0.004 0.001 HIS A 213 PHE 0.011 0.001 PHE A 652 TYR 0.007 0.001 TYR A 164 ARG 0.008 0.000 ARG A 54 *********************** 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 79 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.176 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 166 ASP cc_start: 0.9199 (m-30) cc_final: 0.8914 (p0) REVERT: A 229 ARG cc_start: 0.8028 (mmp-170) cc_final: 0.7782 (mmm160) REVERT: A 231 PHE cc_start: 0.8135 (m-80) cc_final: 0.7665 (m-10) REVERT: A 257 MET cc_start: -0.1416 (mtt) cc_final: -0.2354 (mtt) REVERT: A 266 ASP cc_start: 0.9321 (m-30) cc_final: 0.8736 (t70) REVERT: A 279 ASN cc_start: 0.8932 (m-40) cc_final: 0.8703 (m-40) REVERT: A 293 ARG cc_start: 0.9109 (ttt-90) cc_final: 0.8727 (ttm110) REVERT: A 441 ARG cc_start: 0.7431 (ttt180) cc_final: 0.7163 (ttt180) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.2693 time to fit residues: 26.8026 Evaluate side-chains 62 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 9.9990 chunk 41 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 39 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 8 optimal weight: 0.0970 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 HIS ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 561 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.148023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.117284 restraints weight = 20701.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.118113 restraints weight = 19170.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.118856 restraints weight = 18184.344| |-----------------------------------------------------------------------------| r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5092 Z= 0.196 Angle : 0.605 8.331 6928 Z= 0.311 Chirality : 0.042 0.147 736 Planarity : 0.005 0.042 920 Dihedral : 5.181 20.563 696 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 19.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % 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: -1.64 (0.34), residues: 618 helix: -0.88 (0.27), residues: 334 sheet: -1.71 (1.85), residues: 10 loop : -1.18 (0.41), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 286 HIS 0.005 0.001 HIS A 428 PHE 0.014 0.002 PHE A 241 TYR 0.011 0.002 TYR A 164 ARG 0.009 0.001 ARG A 413 *********************** 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 74 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.830 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 31 ARG cc_start: 0.9274 (mpt180) cc_final: 0.8931 (mpt180) REVERT: A 183 MET cc_start: 0.5643 (tpp) cc_final: 0.5321 (tpt) REVERT: A 231 PHE cc_start: 0.8099 (m-80) cc_final: 0.7594 (m-10) REVERT: A 257 MET cc_start: -0.1108 (mtt) cc_final: -0.2179 (mtt) REVERT: A 266 ASP cc_start: 0.9194 (m-30) cc_final: 0.8650 (t70) REVERT: A 279 ASN cc_start: 0.8949 (m-40) cc_final: 0.8700 (m-40) REVERT: A 441 ARG cc_start: 0.7537 (ttt180) cc_final: 0.7281 (ttt180) outliers start: 0 outliers final: 0 residues processed: 74 average time/residue: 0.2618 time to fit residues: 24.0209 Evaluate side-chains 62 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.152101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.121977 restraints weight = 19946.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.122995 restraints weight = 18614.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.123753 restraints weight = 17674.081| |-----------------------------------------------------------------------------| r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5092 Z= 0.169 Angle : 0.614 11.865 6928 Z= 0.308 Chirality : 0.042 0.145 736 Planarity : 0.005 0.048 920 Dihedral : 5.128 20.977 696 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 1.00 % 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: -1.63 (0.34), residues: 618 helix: -0.88 (0.27), residues: 339 sheet: -1.82 (1.71), residues: 10 loop : -1.16 (0.40), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 604 HIS 0.003 0.001 HIS A 213 PHE 0.012 0.001 PHE A 308 TYR 0.018 0.001 TYR A 368 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 78 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.568 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 31 ARG cc_start: 0.9205 (mpt180) cc_final: 0.8835 (mmt180) REVERT: A 166 ASP cc_start: 0.9206 (m-30) cc_final: 0.8890 (p0) REVERT: A 183 MET cc_start: 0.5564 (tpp) cc_final: 0.5242 (tpt) REVERT: A 231 PHE cc_start: 0.8098 (m-80) cc_final: 0.7628 (m-10) REVERT: A 257 MET cc_start: -0.1195 (mtt) cc_final: -0.2209 (mtt) REVERT: A 266 ASP cc_start: 0.9199 (m-30) cc_final: 0.8684 (t70) REVERT: A 279 ASN cc_start: 0.8898 (m-40) cc_final: 0.8650 (m-40) REVERT: A 293 ARG cc_start: 0.9074 (ttt-90) cc_final: 0.8664 (tpp80) REVERT: A 441 ARG cc_start: 0.7405 (ttt180) cc_final: 0.7164 (ttt180) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2418 time to fit residues: 23.8855 Evaluate side-chains 61 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 44 optimal weight: 0.0040 chunk 48 optimal weight: 9.9990 chunk 7 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 overall best weight: 0.5794 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.156190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.126774 restraints weight = 19375.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.128164 restraints weight = 17632.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.128996 restraints weight = 16311.898| |-----------------------------------------------------------------------------| r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.6430 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= 0.158 Angle : 0.636 12.423 6928 Z= 0.316 Chirality : 0.043 0.238 736 Planarity : 0.005 0.059 920 Dihedral : 5.106 27.747 696 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % 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: -1.63 (0.34), residues: 618 helix: -0.80 (0.27), residues: 344 sheet: -2.10 (1.57), residues: 10 loop : -1.27 (0.40), residues: 264 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 0.018 0.001 PHE A 271 TYR 0.008 0.001 TYR A 164 ARG 0.008 0.001 ARG A 301 ********************** 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 78 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.542 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 28 VAL cc_start: 0.9156 (t) cc_final: 0.8840 (m) REVERT: A 31 ARG cc_start: 0.9175 (mpt180) cc_final: 0.8813 (mmt180) REVERT: A 166 ASP cc_start: 0.9171 (m-30) cc_final: 0.8943 (p0) REVERT: A 183 MET cc_start: 0.5373 (tpp) cc_final: 0.5058 (tpt) REVERT: A 231 PHE cc_start: 0.8094 (m-80) cc_final: 0.7675 (m-10) REVERT: A 257 MET cc_start: -0.1522 (mtt) cc_final: -0.2311 (mtt) REVERT: A 266 ASP cc_start: 0.9213 (m-30) cc_final: 0.8676 (t70) REVERT: A 279 ASN cc_start: 0.8839 (m-40) cc_final: 0.8595 (m-40) REVERT: A 293 ARG cc_start: 0.9061 (ttt-90) cc_final: 0.8629 (tpp80) REVERT: A 378 MET cc_start: 0.3776 (tpp) cc_final: 0.3547 (ttt) REVERT: A 441 ARG cc_start: 0.7394 (ttt180) cc_final: 0.7115 (ttt180) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.2266 time to fit residues: 22.2913 Evaluate side-chains 68 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 29 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 5 optimal weight: 0.0870 chunk 49 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.156805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.126377 restraints weight = 22071.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.127473 restraints weight = 20694.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.128314 restraints weight = 19515.831| |-----------------------------------------------------------------------------| r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 5092 Z= 0.160 Angle : 0.616 11.065 6928 Z= 0.309 Chirality : 0.043 0.248 736 Planarity : 0.004 0.042 920 Dihedral : 4.990 24.136 696 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 0.60 % 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: -1.31 (0.35), residues: 618 helix: -0.63 (0.28), residues: 341 sheet: -2.21 (1.54), residues: 10 loop : -0.97 (0.42), 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 213 PHE 0.020 0.001 PHE A 271 TYR 0.012 0.001 TYR A 406 ARG 0.009 0.001 ARG A 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2034.68 seconds wall clock time: 37 minutes 13.49 seconds (2233.49 seconds total)