Starting phenix.real_space_refine on Tue Mar 3 13:14:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7k1v_22630/03_2026/7k1v_22630.cif Found real_map, /net/cci-nas-00/data/ceres_data/7k1v_22630/03_2026/7k1v_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_2026/7k1v_22630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7k1v_22630/03_2026/7k1v_22630.map" model { file = "/net/cci-nas-00/data/ceres_data/7k1v_22630/03_2026/7k1v_22630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7k1v_22630/03_2026/7k1v_22630.cif" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: 0.96, per 1000 atoms: 0.19 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: 0.32 Conformation dependent library (CDL) restraints added in 337.7 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: 0.17 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: 0.73 Time building geometry restraints manager: 0.44 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.710 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.500 ------------------------------------------------------------------------------- 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= 0.392 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.008 0.001 ARG A 219 TYR 0.032 0.003 TYR A 484 PHE 0.027 0.003 PHE A 652 TRP 0.022 0.003 TRP A 32 HIS 0.008 0.002 HIS A 536 Details of bonding type rmsd covalent geometry : bond 0.00755 ( 5092) covalent geometry : angle 1.11640 ( 6928) hydrogen bonds : bond 0.34366 ( 183) hydrogen bonds : angle 10.86195 ( 531) *********************** 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 : 0.186 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: 0.7757 (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: 0.8167 (tpp80) REVERT: A 366 GLU cc_start: 0.8541 (tp30) cc_final: 0.7929 (tm-30) REVERT: A 397 VAL cc_start: 0.8160 (OUTLIER) cc_final: 0.7925 (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: 0.7096 (pt) REVERT: A 480 GLU cc_start: 0.9158 (tm-30) cc_final: 0.8853 (tm-30) REVERT: A 484 TYR cc_start: 0.8344 (t80) cc_final: 0.7778 (t80) REVERT: A 543 VAL cc_start: 0.1595 (OUTLIER) cc_final: 0.1338 (m) outliers start: 2 outliers final: 0 residues processed: 113 average time/residue: 0.1238 time to fit residues: 16.4160 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 : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 9.9990 chunk 56 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 61 optimal weight: 0.0770 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS A 227 ASN A 346 GLN A 365 GLN A 493 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.157493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.123896 restraints weight = 19004.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.125073 restraints weight = 17499.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.126279 restraints weight = 16398.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.126983 restraints weight = 15487.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.127997 restraints weight = 14725.909| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5092 Z= 0.144 Angle : 0.686 7.576 6928 Z= 0.363 Chirality : 0.044 0.134 736 Planarity : 0.005 0.050 920 Dihedral : 6.778 26.952 696 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 0.00 % Allowed : 4.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.70 (0.30), residues: 618 helix: -2.59 (0.22), residues: 314 sheet: -3.84 (1.50), residues: 10 loop : -2.15 (0.37), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 288 TYR 0.009 0.001 TYR A 454 PHE 0.015 0.002 PHE A 652 TRP 0.019 0.002 TRP A 286 HIS 0.007 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 5092) covalent geometry : angle 0.68610 ( 6928) hydrogen bonds : bond 0.06028 ( 183) hydrogen bonds : angle 7.07374 ( 531) *********************** 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 : 0.170 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: 0.8513 (m-10) cc_final: 0.8278 (m-10) REVERT: A 231 PHE cc_start: 0.8477 (m-80) cc_final: 0.8133 (m-10) REVERT: A 266 ASP cc_start: 0.9172 (m-30) cc_final: 0.8664 (t0) REVERT: A 293 ARG cc_start: 0.9060 (ttt-90) cc_final: 0.8605 (tpp80) REVERT: A 431 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8701 (pp20) REVERT: A 462 ILE cc_start: 0.7141 (pt) cc_final: 0.6865 (pt) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.1054 time to fit residues: 11.6948 Evaluate side-chains 69 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 54 optimal weight: 4.9990 chunk 51 optimal weight: 0.3980 chunk 57 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 52 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN A 150 HIS A 365 GLN ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 460 ASN A 493 HIS A 582 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.157665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.124066 restraints weight = 19349.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.125371 restraints weight = 17848.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 14)----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.126146 restraints weight = 16670.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.127159 restraints weight = 15887.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.127948 restraints weight = 15200.560| |-----------------------------------------------------------------------------| r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5092 Z= 0.124 Angle : 0.627 10.499 6928 Z= 0.327 Chirality : 0.042 0.175 736 Planarity : 0.004 0.044 920 Dihedral : 6.004 25.141 696 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.32), residues: 618 helix: -2.00 (0.25), residues: 324 sheet: -3.41 (1.68), residues: 10 loop : -1.77 (0.39), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 54 TYR 0.021 0.001 TYR A 484 PHE 0.013 0.002 PHE A 652 TRP 0.016 0.002 TRP A 298 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 5092) covalent geometry : angle 0.62742 ( 6928) hydrogen bonds : bond 0.04807 ( 183) hydrogen bonds : angle 6.44781 ( 531) *********************** 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 86 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.195 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 214 TRP cc_start: 0.8626 (m-10) cc_final: 0.8298 (m-10) REVERT: A 231 PHE cc_start: 0.8445 (m-80) cc_final: 0.8143 (m-10) REVERT: A 257 MET cc_start: -0.1206 (mtt) cc_final: -0.2684 (mtt) REVERT: A 266 ASP cc_start: 0.9211 (m-30) cc_final: 0.8734 (t0) REVERT: A 293 ARG cc_start: 0.9123 (ttt-90) cc_final: 0.8619 (tpp80) REVERT: A 462 ILE cc_start: 0.6829 (pt) cc_final: 0.6526 (pt) REVERT: A 582 ASN cc_start: 0.9464 (m-40) cc_final: 0.9109 (t0) REVERT: A 604 TRP cc_start: 0.4911 (m100) cc_final: 0.4685 (m100) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.0901 time to fit residues: 9.5798 Evaluate side-chains 59 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 32 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 6.9990 chunk 27 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- 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** A 561 ASN A 663 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.151877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.117289 restraints weight = 18574.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.118603 restraints weight = 17069.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.119680 restraints weight = 15935.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.120442 restraints weight = 15069.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.121351 restraints weight = 14302.621| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.4647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5092 Z= 0.153 Angle : 0.632 9.682 6928 Z= 0.335 Chirality : 0.043 0.160 736 Planarity : 0.005 0.043 920 Dihedral : 5.911 21.700 696 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.12 % Favored : 92.88 % Rotamer: Outliers : 0.20 % Allowed : 4.99 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.33), residues: 618 helix: -1.73 (0.25), residues: 327 sheet: -2.96 (1.66), residues: 10 loop : -1.49 (0.40), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 54 TYR 0.013 0.002 TYR A 164 PHE 0.015 0.002 PHE A 652 TRP 0.027 0.002 TRP A 286 HIS 0.005 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 5092) covalent geometry : angle 0.63203 ( 6928) hydrogen bonds : bond 0.04776 ( 183) hydrogen bonds : angle 6.47186 ( 531) *********************** 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 84 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.186 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 214 TRP cc_start: 0.8584 (m-10) cc_final: 0.8061 (m-10) REVERT: A 231 PHE cc_start: 0.8357 (m-80) cc_final: 0.7978 (m-10) REVERT: A 257 MET cc_start: -0.0583 (mtt) cc_final: -0.2218 (mtt) REVERT: A 266 ASP cc_start: 0.9238 (m-30) cc_final: 0.8782 (t0) REVERT: A 293 ARG cc_start: 0.9077 (ttt-90) cc_final: 0.8609 (tpp80) REVERT: A 582 ASN cc_start: 0.9501 (m-40) cc_final: 0.9104 (t0) REVERT: A 602 GLN cc_start: 0.9284 (mp10) cc_final: 0.8999 (mp10) outliers start: 1 outliers final: 0 residues processed: 83 average time/residue: 0.0782 time to fit residues: 8.1711 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 : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 39 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 30 optimal weight: 6.9990 chunk 29 optimal weight: 0.0870 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.0010 chunk 25 optimal weight: 2.9990 chunk 26 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 overall best weight: 0.7166 ------------------------------------------------------------------------------- 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 ** A 456 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.157836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.126395 restraints weight = 19674.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.127426 restraints weight = 18160.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.128751 restraints weight = 16995.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.129550 restraints weight = 15998.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.130366 restraints weight = 15127.812| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7479 moved from start: 0.5089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5092 Z= 0.115 Angle : 0.598 10.844 6928 Z= 0.308 Chirality : 0.042 0.163 736 Planarity : 0.004 0.040 920 Dihedral : 5.585 20.644 696 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.33), residues: 618 helix: -1.40 (0.27), residues: 319 sheet: -2.47 (1.74), residues: 10 loop : -1.19 (0.39), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.011 0.001 TYR A 164 PHE 0.013 0.002 PHE A 151 TRP 0.018 0.002 TRP A 286 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 5092) covalent geometry : angle 0.59826 ( 6928) hydrogen bonds : bond 0.03986 ( 183) hydrogen bonds : angle 6.10212 ( 531) *********************** 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 82 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 0.191 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 166 ASP cc_start: 0.9206 (m-30) cc_final: 0.8921 (p0) REVERT: A 231 PHE cc_start: 0.8116 (m-80) cc_final: 0.7777 (m-10) REVERT: A 257 MET cc_start: -0.1300 (mtt) cc_final: -0.2398 (mtt) REVERT: A 266 ASP cc_start: 0.9072 (m-30) cc_final: 0.8563 (t0) REVERT: A 293 ARG cc_start: 0.9061 (ttt-90) cc_final: 0.8607 (tpp80) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.0916 time to fit residues: 9.3502 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 : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 45 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 43 optimal weight: 6.9990 chunk 26 optimal weight: 0.0040 chunk 4 optimal weight: 0.5980 chunk 61 optimal weight: 0.0770 chunk 54 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 ASN A 663 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.160685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126950 restraints weight = 18911.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 19)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126952 restraints weight = 17500.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126952 restraints weight = 17498.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126952 restraints weight = 17498.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.126952 restraints weight = 17498.937| |-----------------------------------------------------------------------------| r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.5516 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= 0.108 Angle : 0.590 9.430 6928 Z= 0.304 Chirality : 0.042 0.178 736 Planarity : 0.004 0.040 920 Dihedral : 5.275 22.013 696 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.34), residues: 618 helix: -1.17 (0.27), residues: 325 sheet: -2.01 (1.78), residues: 10 loop : -0.99 (0.41), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 126 TYR 0.013 0.001 TYR A 575 PHE 0.017 0.001 PHE A 598 TRP 0.018 0.002 TRP A 286 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 5092) covalent geometry : angle 0.59032 ( 6928) hydrogen bonds : bond 0.03684 ( 183) hydrogen bonds : angle 6.10789 ( 531) *********************** 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 : 0.188 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 125 GLN cc_start: 0.9080 (pt0) cc_final: 0.8872 (pt0) REVERT: A 166 ASP cc_start: 0.9235 (m-30) cc_final: 0.9009 (p0) REVERT: A 231 PHE cc_start: 0.7900 (m-80) cc_final: 0.7630 (m-10) REVERT: A 257 MET cc_start: -0.1704 (mtt) cc_final: -0.2568 (mtt) REVERT: A 266 ASP cc_start: 0.8997 (m-30) cc_final: 0.8489 (t0) REVERT: A 293 ARG cc_start: 0.9056 (ttt-90) cc_final: 0.8588 (tpp80) outliers start: 0 outliers final: 0 residues processed: 76 average time/residue: 0.0908 time to fit residues: 8.6738 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 : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 30 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 43 optimal weight: 0.0010 overall best weight: 1.1392 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.154794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.122675 restraints weight = 19481.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.123730 restraints weight = 18231.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.124396 restraints weight = 17208.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.125297 restraints weight = 16508.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.125297 restraints weight = 15883.081| |-----------------------------------------------------------------------------| r_work (final): 0.4099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.5671 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= 0.120 Angle : 0.591 8.395 6928 Z= 0.305 Chirality : 0.042 0.183 736 Planarity : 0.004 0.041 920 Dihedral : 5.185 20.952 696 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.65 (0.34), residues: 618 helix: -1.05 (0.27), residues: 325 sheet: -1.42 (1.91), residues: 10 loop : -0.96 (0.41), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 126 TYR 0.011 0.001 TYR A 164 PHE 0.014 0.002 PHE A 308 TRP 0.021 0.002 TRP A 286 HIS 0.005 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5092) covalent geometry : angle 0.59120 ( 6928) hydrogen bonds : bond 0.03709 ( 183) hydrogen bonds : angle 6.02475 ( 531) *********************** 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 73 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.182 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 166 ASP cc_start: 0.9201 (m-30) cc_final: 0.8933 (p0) REVERT: A 231 PHE cc_start: 0.8004 (m-80) cc_final: 0.7640 (m-10) REVERT: A 257 MET cc_start: -0.1715 (mtt) cc_final: -0.2565 (mtt) REVERT: A 266 ASP cc_start: 0.9029 (m-30) cc_final: 0.8491 (t0) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.0802 time to fit residues: 7.4147 Evaluate side-chains 60 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.5980 chunk 22 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 7 optimal weight: 7.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- 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 169 HIS A 319 GLN ** A 365 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 ASN ** A 511 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.139728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.109300 restraints weight = 20792.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.110154 restraints weight = 19381.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.111115 restraints weight = 18240.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.111683 restraints weight = 17473.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.112013 restraints weight = 16904.477| |-----------------------------------------------------------------------------| r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 5092 Z= 0.227 Angle : 0.727 9.813 6928 Z= 0.386 Chirality : 0.046 0.180 736 Planarity : 0.005 0.043 920 Dihedral : 5.993 25.008 696 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 26.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 0.20 % Allowed : 1.20 % Favored : 98.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.85 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.34), residues: 618 helix: -1.19 (0.27), residues: 311 sheet: -1.94 (1.73), residues: 10 loop : -1.01 (0.40), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 219 TYR 0.019 0.002 TYR A 575 PHE 0.019 0.003 PHE A 241 TRP 0.034 0.003 TRP A 286 HIS 0.005 0.002 HIS A 195 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 5092) covalent geometry : angle 0.72700 ( 6928) hydrogen bonds : bond 0.05295 ( 183) hydrogen bonds : angle 6.57124 ( 531) *********************** 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 80 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 0.199 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: 0.5934 (tpp) cc_final: 0.5695 (tpt) REVERT: A 231 PHE cc_start: 0.8255 (m-80) cc_final: 0.7827 (m-10) REVERT: A 246 TRP cc_start: 0.8318 (t60) cc_final: 0.8070 (t60) REVERT: A 257 MET cc_start: -0.0399 (mtt) cc_final: -0.1727 (mtt) REVERT: A 266 ASP cc_start: 0.9237 (m-30) cc_final: 0.8689 (t70) REVERT: A 447 THR cc_start: 0.8458 (m) cc_final: 0.8121 (m) REVERT: A 462 ILE cc_start: 0.7405 (pt) cc_final: 0.7091 (pt) REVERT: A 470 GLN cc_start: 0.9551 (tt0) cc_final: 0.9293 (tt0) outliers start: 1 outliers final: 0 residues processed: 80 average time/residue: 0.0832 time to fit residues: 8.5685 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 : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 2 optimal weight: 0.4980 chunk 44 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 58 optimal weight: 0.0030 chunk 39 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- 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 502 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 511 ASN ** 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 = 0.4343 r_free = 0.4343 target = 0.156623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.125241 restraints weight = 20156.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.126372 restraints weight = 18852.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 13)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.127028 restraints weight = 17720.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.127671 restraints weight = 16945.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.128480 restraints weight = 16307.282| |-----------------------------------------------------------------------------| r_work (final): 0.4086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7531 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5092 Z= 0.115 Angle : 0.655 11.704 6928 Z= 0.326 Chirality : 0.044 0.193 736 Planarity : 0.005 0.041 920 Dihedral : 5.415 22.159 696 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.33), residues: 618 helix: -1.07 (0.26), residues: 338 sheet: -2.27 (1.58), residues: 10 loop : -1.14 (0.40), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 126 TYR 0.013 0.001 TYR A 368 PHE 0.022 0.002 PHE A 598 TRP 0.024 0.002 TRP A 286 HIS 0.006 0.001 HIS A 493 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 5092) covalent geometry : angle 0.65499 ( 6928) hydrogen bonds : bond 0.03671 ( 183) hydrogen bonds : angle 6.05135 ( 531) *********************** 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 72 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ASP cc_start: 0.9256 (m-30) cc_final: 0.9015 (p0) REVERT: A 183 MET cc_start: 0.5318 (tpp) cc_final: 0.4983 (tpt) REVERT: A 231 PHE cc_start: 0.8252 (m-80) cc_final: 0.7918 (m-10) REVERT: A 246 TRP cc_start: 0.8326 (t60) cc_final: 0.7984 (t60) REVERT: A 257 MET cc_start: -0.1545 (mtt) cc_final: -0.2221 (mtt) REVERT: A 266 ASP cc_start: 0.9214 (m-30) cc_final: 0.8696 (t70) REVERT: A 293 ARG cc_start: 0.9086 (ttt-90) cc_final: 0.8634 (tpp80) REVERT: A 447 THR cc_start: 0.8358 (m) cc_final: 0.8137 (m) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.0762 time to fit residues: 7.1057 Evaluate side-chains 59 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 34 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 502 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 = 0.4321 r_free = 0.4321 target = 0.153683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.121774 restraints weight = 20399.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.123019 restraints weight = 18950.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.124140 restraints weight = 17757.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.125235 restraints weight = 16433.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.125791 restraints weight = 15784.275| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.6299 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= 0.117 Angle : 0.634 11.227 6928 Z= 0.317 Chirality : 0.043 0.172 736 Planarity : 0.004 0.042 920 Dihedral : 5.228 22.255 696 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 15.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.33), residues: 618 helix: -0.87 (0.27), residues: 330 sheet: -2.09 (1.55), residues: 10 loop : -1.12 (0.39), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 301 TYR 0.011 0.001 TYR A 164 PHE 0.014 0.001 PHE A 241 TRP 0.020 0.002 TRP A 286 HIS 0.004 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 5092) covalent geometry : angle 0.63418 ( 6928) hydrogen bonds : bond 0.03609 ( 183) hydrogen bonds : angle 5.96851 ( 531) ********************** 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 69 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.173 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 166 ASP cc_start: 0.9248 (m-30) cc_final: 0.9023 (p0) REVERT: A 183 MET cc_start: 0.5370 (tpp) cc_final: 0.5077 (tpt) REVERT: A 231 PHE cc_start: 0.8170 (m-80) cc_final: 0.7767 (m-10) REVERT: A 246 TRP cc_start: 0.8184 (t60) cc_final: 0.7866 (t60) REVERT: A 257 MET cc_start: -0.1629 (mtt) cc_final: -0.2269 (mtt) REVERT: A 266 ASP cc_start: 0.9232 (m-30) cc_final: 0.8698 (t70) REVERT: A 293 ARG cc_start: 0.9100 (ttt-90) cc_final: 0.8656 (tpp80) REVERT: A 446 MET cc_start: 0.7108 (ppp) cc_final: 0.6900 (ppp) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0788 time to fit residues: 7.0656 Evaluate side-chains 58 residues out of total 501 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 0.0060 chunk 17 optimal weight: 0.2980 chunk 48 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 38 optimal weight: 6.9990 chunk 56 optimal weight: 0.2980 chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 40 optimal weight: 0.8980 overall best weight: 0.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 HIS A 125 GLN A 663 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.158339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.126586 restraints weight = 20635.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.127649 restraints weight = 19343.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4102 r_free = 0.4102 target = 0.128384 restraints weight = 18297.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.129369 restraints weight = 17383.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.129805 restraints weight = 16762.598| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.6693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5092 Z= 0.109 Angle : 0.638 10.555 6928 Z= 0.318 Chirality : 0.043 0.161 736 Planarity : 0.004 0.042 920 Dihedral : 5.082 21.981 696 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 13.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.20 % Allowed : 0.20 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.66 (0.33), residues: 618 helix: -0.87 (0.27), residues: 341 sheet: -2.47 (1.46), residues: 10 loop : -1.19 (0.40), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 301 TYR 0.014 0.001 TYR A 506 PHE 0.018 0.001 PHE A 271 TRP 0.016 0.002 TRP A 286 HIS 0.003 0.001 HIS A 213 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 5092) covalent geometry : angle 0.63813 ( 6928) hydrogen bonds : bond 0.03600 ( 183) hydrogen bonds : angle 5.94556 ( 531) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 962.20 seconds wall clock time: 17 minutes 15.73 seconds (1035.73 seconds total)