Starting phenix.real_space_refine on Wed Feb 12 20:19:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8et7_28587/02_2025/8et7_28587_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8et7_28587/02_2025/8et7_28587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8et7_28587/02_2025/8et7_28587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8et7_28587/02_2025/8et7_28587.map" model { file = "/net/cci-nas-00/data/ceres_data/8et7_28587/02_2025/8et7_28587_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8et7_28587/02_2025/8et7_28587_trim.cif" } resolution = 3.77 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= 0.003 sd= 0.048 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: 5 Type Number sf(0) Gaussians S 29 5.16 5 C 2698 2.51 5 N 670 2.21 5 O 707 1.98 5 H 4007 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8111 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 8064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 8064 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 25, 'TRANS': 506} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'GLU:plan': 7, 'ARG:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 54 Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'2PM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.10, per 1000 atoms: 0.51 Number of scatterers: 8111 At special positions: 0 Unit cell: (112.32, 56.16, 73.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 O 707 8.00 N 670 7.00 C 2698 6.00 H 4007 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG B 1 " - " ASN A 71 " Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 739.7 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 978 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 1 sheets defined 77.4% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'A' and resid 3 through 12 Processing helix chain 'A' and resid 15 through 32 removed outlier: 3.501A pdb=" N ALA A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N PHE A 32 " --> pdb=" O LEU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 32 through 38 removed outlier: 4.003A pdb=" N GLY A 38 " --> pdb=" O PRO A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.979A pdb=" N ALA A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ARG A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N CYS A 62 " --> pdb=" O LEU A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 74 removed outlier: 3.659A pdb=" N VAL A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 89 removed outlier: 3.572A pdb=" N CYS A 88 " --> pdb=" O PHE A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 111 removed outlier: 4.174A pdb=" N ALA A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 139 Processing helix chain 'A' and resid 145 through 166 removed outlier: 4.369A pdb=" N ASP A 149 " --> pdb=" O SER A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 173 removed outlier: 3.618A pdb=" N ALA A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 194 removed outlier: 3.720A pdb=" N CYS A 178 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR A 183 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA A 194 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 228 removed outlier: 4.174A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.956A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 258 Processing helix chain 'A' and resid 260 through 278 Proline residue: A 271 - end of helix removed outlier: 3.784A pdb=" N LEU A 274 " --> pdb=" O LEU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 281 No H-bonds generated for 'chain 'A' and resid 279 through 281' Processing helix chain 'A' and resid 285 through 292 Processing helix chain 'A' and resid 294 through 310 Processing helix chain 'A' and resid 314 through 320 removed outlier: 3.678A pdb=" N LEU A 317 " --> pdb=" O PRO A 314 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 318 " --> pdb=" O ALA A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 339 removed outlier: 3.911A pdb=" N ARG A 339 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 367 Processing helix chain 'A' and resid 374 through 385 Processing helix chain 'A' and resid 385 through 401 removed outlier: 4.186A pdb=" N ALA A 389 " --> pdb=" O VAL A 385 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ASP A 398 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ARG A 399 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 403 through 423 Processing helix chain 'A' and resid 428 through 457 removed outlier: 3.896A pdb=" N ILE A 432 " --> pdb=" O HIS A 428 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N THR A 433 " --> pdb=" O TRP A 429 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N TYR A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 461 through 491 removed outlier: 4.014A pdb=" N LEU A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N CYS A 473 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ASP A 474 " --> pdb=" O SER A 470 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.857A pdb=" N GLU A 489 " --> pdb=" O PHE A 485 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 490 " --> pdb=" O ARG A 486 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 510 removed outlier: 3.637A pdb=" N ILE A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 513 No H-bonds generated for 'chain 'A' and resid 511 through 513' Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.682A pdb=" N ASN A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 48 through 49 264 hydrogen bonds defined for protein. 777 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: 2.91 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3998 1.03 - 1.23: 12 1.23 - 1.42: 1766 1.42 - 1.62: 2401 1.62 - 1.81: 43 Bond restraints: 8220 Sorted by residual: bond pdb=" C15 2PM A 601 " pdb=" N1 2PM A 601 " ideal model delta sigma weight residual 1.448 1.512 -0.064 2.00e-02 2.50e+03 1.04e+01 bond pdb=" C14 2PM A 601 " pdb=" C15 2PM A 601 " ideal model delta sigma weight residual 1.513 1.572 -0.059 2.00e-02 2.50e+03 8.83e+00 bond pdb=" C16 2PM A 601 " pdb=" N1 2PM A 601 " ideal model delta sigma weight residual 1.446 1.504 -0.058 2.00e-02 2.50e+03 8.28e+00 bond pdb=" C17 2PM A 601 " pdb=" N1 2PM A 601 " ideal model delta sigma weight residual 1.446 1.492 -0.046 2.00e-02 2.50e+03 5.37e+00 bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.85e+00 ... (remaining 8215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.98: 13569 0.98 - 1.96: 1183 1.96 - 2.95: 44 2.95 - 3.93: 18 3.93 - 4.91: 10 Bond angle restraints: 14824 Sorted by residual: angle pdb=" N VAL A 212 " pdb=" CA VAL A 212 " pdb=" C VAL A 212 " ideal model delta sigma weight residual 109.34 113.83 -4.49 2.08e+00 2.31e-01 4.66e+00 angle pdb=" C15 2PM A 601 " pdb=" N1 2PM A 601 " pdb=" C16 2PM A 601 " ideal model delta sigma weight residual 112.87 108.18 4.69 3.00e+00 1.11e-01 2.44e+00 angle pdb=" N CYS A 281 " pdb=" CA CYS A 281 " pdb=" C CYS A 281 " ideal model delta sigma weight residual 110.97 112.63 -1.66 1.09e+00 8.42e-01 2.31e+00 angle pdb=" N GLU A 386 " pdb=" CA GLU A 386 " pdb=" C GLU A 386 " ideal model delta sigma weight residual 111.69 113.52 -1.83 1.23e+00 6.61e-01 2.20e+00 angle pdb=" N ILE A 461 " pdb=" CA ILE A 461 " pdb=" C ILE A 461 " ideal model delta sigma weight residual 109.34 112.37 -3.03 2.08e+00 2.31e-01 2.13e+00 ... (remaining 14819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.24: 3622 17.24 - 34.48: 211 34.48 - 51.71: 74 51.71 - 68.95: 33 68.95 - 86.19: 2 Dihedral angle restraints: 3942 sinusoidal: 2086 harmonic: 1856 Sorted by residual: dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 60.20 32.80 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -113.35 27.35 1 1.00e+01 1.00e-02 1.07e+01 dihedral pdb=" CA LEU A 23 " pdb=" CB LEU A 23 " pdb=" CG LEU A 23 " pdb=" CD1 LEU A 23 " ideal model delta sinusoidal sigma weight residual 180.00 129.98 50.02 3 1.50e+01 4.44e-03 8.85e+00 ... (remaining 3939 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 430 0.025 - 0.051: 158 0.051 - 0.076: 58 0.076 - 0.102: 20 0.102 - 0.127: 8 Chirality restraints: 674 Sorted by residual: chirality pdb=" CA VAL A 74 " pdb=" N VAL A 74 " pdb=" C VAL A 74 " pdb=" CB VAL A 74 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.03e-01 chirality pdb=" CA THR A 480 " pdb=" N THR A 480 " pdb=" C THR A 480 " pdb=" CB THR A 480 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.12 2.00e-01 2.50e+01 3.78e-01 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 71 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.52 0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 671 not shown) Planarity restraints: 1216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 282 " 0.021 5.00e-02 4.00e+02 3.11e-02 1.54e+00 pdb=" N PRO A 283 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 283 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 283 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 480 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 481 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 481 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 481 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 270 " 0.018 5.00e-02 4.00e+02 2.79e-02 1.25e+00 pdb=" N PRO A 271 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 271 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 271 " 0.016 5.00e-02 4.00e+02 ... (remaining 1213 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 719 2.24 - 2.83: 17899 2.83 - 3.42: 20994 3.42 - 4.01: 27283 4.01 - 4.60: 42172 Nonbonded interactions: 109067 Sorted by model distance: nonbonded pdb=" O ILE A 305 " pdb="HD22 ASN A 309 " model vdw 1.650 2.450 nonbonded pdb=" OE1 GLN A 342 " pdb=" H GLN A 342 " model vdw 1.683 2.450 nonbonded pdb=" O ARG A 90 " pdb=" H GLY A 119 " model vdw 1.766 2.450 nonbonded pdb=" H ARG A 175 " pdb=" OE2 GLU A 284 " model vdw 1.771 2.450 nonbonded pdb=" O VAL A 249 " pdb=" HG SER A 252 " model vdw 1.785 2.450 ... (remaining 109062 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.370 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: 0.140 Extract box with map and model: 0.260 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 21.020 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 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 : 0.003 0.064 4213 Z= 0.222 Angle : 0.493 4.908 5749 Z= 0.259 Chirality : 0.034 0.127 674 Planarity : 0.003 0.031 709 Dihedral : 11.060 86.190 1481 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.24 % Allowed : 5.19 % Favored : 94.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.38), residues: 530 helix: 2.32 (0.28), residues: 345 sheet: None (None), residues: 0 loop : -0.86 (0.48), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 288 HIS 0.002 0.000 HIS A 48 PHE 0.014 0.001 PHE A 275 TYR 0.012 0.001 TYR A 240 ARG 0.002 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 182 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 181 time to evaluate : 0.545 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 19 LYS cc_start: 0.8206 (mttt) cc_final: 0.7456 (mtmm) REVERT: A 45 THR cc_start: 0.9113 (m) cc_final: 0.8737 (p) REVERT: A 70 LEU cc_start: 0.8765 (tp) cc_final: 0.8520 (tp) REVERT: A 209 GLN cc_start: 0.8718 (tt0) cc_final: 0.8462 (tt0) outliers start: 1 outliers final: 0 residues processed: 182 average time/residue: 0.3021 time to fit residues: 69.8586 Evaluate side-chains 125 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 346 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.176770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.151853 restraints weight = 18438.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.158232 restraints weight = 7269.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.162033 restraints weight = 3796.973| |-----------------------------------------------------------------------------| r_work (final): 0.3966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4213 Z= 0.203 Angle : 0.558 4.731 5749 Z= 0.299 Chirality : 0.035 0.122 674 Planarity : 0.004 0.035 709 Dihedral : 5.154 39.063 620 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.12 % Allowed : 14.15 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.37), residues: 530 helix: 2.14 (0.27), residues: 355 sheet: None (None), residues: 0 loop : -0.85 (0.50), residues: 175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 491 HIS 0.004 0.001 HIS A 367 PHE 0.019 0.002 PHE A 275 TYR 0.012 0.001 TYR A 240 ARG 0.003 0.000 ARG A 51 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 130 time to evaluate : 0.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9248 (m) cc_final: 0.8830 (p) REVERT: A 347 THR cc_start: 0.8051 (m) cc_final: 0.7705 (m) REVERT: A 364 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8392 (tt) outliers start: 9 outliers final: 6 residues processed: 134 average time/residue: 0.2390 time to fit residues: 42.9086 Evaluate side-chains 123 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 38 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 297 GLN A 346 HIS A 367 HIS ** A 453 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 = 0.4029 r_free = 0.4029 target = 0.170675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145940 restraints weight = 19009.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.152067 restraints weight = 7465.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.155760 restraints weight = 3930.692| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.4134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4213 Z= 0.279 Angle : 0.593 4.843 5749 Z= 0.327 Chirality : 0.036 0.128 674 Planarity : 0.005 0.058 709 Dihedral : 5.381 38.972 620 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.54 % Allowed : 13.92 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.37), residues: 530 helix: 2.00 (0.27), residues: 354 sheet: None (None), residues: 0 loop : -1.29 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 429 HIS 0.011 0.002 HIS A 123 PHE 0.016 0.001 PHE A 275 TYR 0.015 0.002 TYR A 221 ARG 0.003 0.001 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9264 (m) cc_final: 0.8911 (p) REVERT: A 146 TRP cc_start: 0.8346 (p-90) cc_final: 0.8027 (p90) REVERT: A 193 MET cc_start: 0.8681 (ttp) cc_final: 0.8465 (ttt) REVERT: A 364 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8440 (tt) REVERT: A 479 ILE cc_start: 0.9163 (tp) cc_final: 0.8908 (tt) outliers start: 15 outliers final: 11 residues processed: 133 average time/residue: 0.2319 time to fit residues: 41.6223 Evaluate side-chains 126 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 424 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 48 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS ** A 453 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 = 0.4041 r_free = 0.4041 target = 0.172286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.148156 restraints weight = 18971.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.154155 restraints weight = 7328.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157782 restraints weight = 3833.775| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4213 Z= 0.169 Angle : 0.531 4.781 5749 Z= 0.279 Chirality : 0.034 0.125 674 Planarity : 0.004 0.035 709 Dihedral : 5.101 36.981 620 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.30 % Allowed : 17.45 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.38), residues: 530 helix: 2.19 (0.27), residues: 357 sheet: None (None), residues: 0 loop : -1.09 (0.50), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 429 HIS 0.005 0.001 HIS A 367 PHE 0.016 0.001 PHE A 275 TYR 0.014 0.001 TYR A 240 ARG 0.004 0.000 ARG A 233 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 130 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 116 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9233 (m) cc_final: 0.8860 (p) REVERT: A 193 MET cc_start: 0.8624 (ttp) cc_final: 0.8403 (ttt) REVERT: A 364 LEU cc_start: 0.8708 (OUTLIER) cc_final: 0.8426 (tt) REVERT: A 455 GLU cc_start: 0.8823 (tp30) cc_final: 0.8420 (tp30) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.2626 time to fit residues: 42.8078 Evaluate side-chains 124 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 111 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 411 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 42 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS ** A 453 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 = 0.4044 r_free = 0.4044 target = 0.172167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.147590 restraints weight = 18780.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.153642 restraints weight = 7290.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.157315 restraints weight = 3808.958| |-----------------------------------------------------------------------------| r_work (final): 0.3839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4213 Z= 0.181 Angle : 0.525 4.735 5749 Z= 0.277 Chirality : 0.034 0.126 674 Planarity : 0.004 0.033 709 Dihedral : 5.020 36.768 620 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 4.01 % Allowed : 17.45 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.38), residues: 530 helix: 2.25 (0.28), residues: 359 sheet: None (None), residues: 0 loop : -1.01 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 429 HIS 0.005 0.001 HIS A 367 PHE 0.014 0.001 PHE A 275 TYR 0.014 0.001 TYR A 240 ARG 0.004 0.001 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 126 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 109 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9242 (m) cc_final: 0.8891 (p) REVERT: A 193 MET cc_start: 0.8632 (ttp) cc_final: 0.8409 (ttt) REVERT: A 364 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8348 (tt) outliers start: 17 outliers final: 16 residues processed: 118 average time/residue: 0.2451 time to fit residues: 39.6061 Evaluate side-chains 122 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 27 optimal weight: 2.9990 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144105 restraints weight = 18822.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.150028 restraints weight = 7291.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.153662 restraints weight = 3810.647| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.5065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4213 Z= 0.226 Angle : 0.542 4.838 5749 Z= 0.291 Chirality : 0.034 0.130 674 Planarity : 0.004 0.033 709 Dihedral : 5.092 37.504 620 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.77 % Allowed : 17.22 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.38), residues: 530 helix: 2.13 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.16 (0.50), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 429 HIS 0.004 0.001 HIS A 367 PHE 0.013 0.001 PHE A 275 TYR 0.014 0.002 TYR A 72 ARG 0.003 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9265 (m) cc_final: 0.8937 (p) REVERT: A 193 MET cc_start: 0.8670 (ttp) cc_final: 0.8447 (ttt) REVERT: A 364 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8363 (tt) REVERT: A 457 TYR cc_start: 0.8546 (m-80) cc_final: 0.8313 (m-10) outliers start: 16 outliers final: 15 residues processed: 125 average time/residue: 0.2405 time to fit residues: 40.2318 Evaluate side-chains 125 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 411 LEU Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.3980 chunk 32 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 0.0570 chunk 14 optimal weight: 0.0970 chunk 31 optimal weight: 0.4980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS ** A 453 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 = 0.4043 r_free = 0.4043 target = 0.171940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.148243 restraints weight = 18720.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.154138 restraints weight = 7158.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.157745 restraints weight = 3717.474| |-----------------------------------------------------------------------------| r_work (final): 0.3889 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4213 Z= 0.153 Angle : 0.504 4.774 5749 Z= 0.262 Chirality : 0.034 0.126 674 Planarity : 0.004 0.035 709 Dihedral : 4.869 36.514 620 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.54 % Allowed : 18.16 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.38), residues: 530 helix: 2.33 (0.27), residues: 360 sheet: None (None), residues: 0 loop : -1.01 (0.51), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 354 HIS 0.004 0.001 HIS A 367 PHE 0.013 0.001 PHE A 275 TYR 0.013 0.001 TYR A 240 ARG 0.004 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9256 (m) cc_final: 0.8924 (p) REVERT: A 193 MET cc_start: 0.8600 (ttp) cc_final: 0.8390 (ttt) REVERT: A 364 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8350 (tt) REVERT: A 457 TYR cc_start: 0.8524 (m-80) cc_final: 0.8238 (m-10) outliers start: 15 outliers final: 12 residues processed: 116 average time/residue: 0.2207 time to fit residues: 35.2596 Evaluate side-chains 119 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 106 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 139 ASN Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 14 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.0170 chunk 5 optimal weight: 0.8980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.172468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.148726 restraints weight = 18879.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.154671 restraints weight = 7208.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.158276 restraints weight = 3724.843| |-----------------------------------------------------------------------------| r_work (final): 0.3841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 4213 Z= 0.158 Angle : 0.500 4.828 5749 Z= 0.259 Chirality : 0.034 0.127 674 Planarity : 0.004 0.035 709 Dihedral : 4.757 36.615 620 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 3.07 % Allowed : 18.16 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.38), residues: 530 helix: 2.43 (0.27), residues: 359 sheet: None (None), residues: 0 loop : -0.96 (0.51), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 429 HIS 0.003 0.001 HIS A 48 PHE 0.012 0.001 PHE A 275 TYR 0.012 0.001 TYR A 72 ARG 0.003 0.000 ARG A 113 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 125 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 112 time to evaluate : 0.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.9299 (m) cc_final: 0.9021 (p) REVERT: A 193 MET cc_start: 0.8577 (ttp) cc_final: 0.8365 (ttt) REVERT: A 233 ARG cc_start: 0.7630 (ttm110) cc_final: 0.7347 (ttm110) REVERT: A 364 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8286 (tt) outliers start: 13 outliers final: 11 residues processed: 119 average time/residue: 0.2619 time to fit residues: 40.9080 Evaluate side-chains 123 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 111 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.168795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.144063 restraints weight = 19291.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.150004 restraints weight = 7386.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.153713 restraints weight = 3866.643| |-----------------------------------------------------------------------------| r_work (final): 0.3752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.5580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 4213 Z= 0.317 Angle : 0.596 5.126 5749 Z= 0.329 Chirality : 0.036 0.135 674 Planarity : 0.004 0.035 709 Dihedral : 5.083 38.417 620 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.30 % Allowed : 18.40 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.37), residues: 530 helix: 1.88 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.29 (0.50), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 429 HIS 0.003 0.001 HIS A 123 PHE 0.011 0.002 PHE A 275 TYR 0.021 0.002 TYR A 91 ARG 0.002 0.000 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 107 time to evaluate : 0.641 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8982 (m-80) cc_final: 0.8672 (m-80) REVERT: A 45 THR cc_start: 0.9249 (m) cc_final: 0.8985 (p) REVERT: A 364 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8329 (tt) outliers start: 14 outliers final: 13 residues processed: 115 average time/residue: 0.2187 time to fit residues: 34.4152 Evaluate side-chains 120 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 106 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 362 GLN Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 16 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.4980 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.169463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.145675 restraints weight = 18769.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.151551 restraints weight = 7138.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.155180 restraints weight = 3686.917| |-----------------------------------------------------------------------------| r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4213 Z= 0.160 Angle : 0.526 4.839 5749 Z= 0.273 Chirality : 0.035 0.190 674 Planarity : 0.004 0.036 709 Dihedral : 4.913 36.713 620 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 2.83 % Allowed : 19.34 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.38), residues: 530 helix: 2.17 (0.27), residues: 367 sheet: None (None), residues: 0 loop : -0.92 (0.53), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 429 HIS 0.002 0.001 HIS A 123 PHE 0.013 0.001 PHE A 275 TYR 0.029 0.002 TYR A 72 ARG 0.001 0.000 ARG A 206 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 98 is missing expected H atoms. Skipping. Residue LEU 100 is missing expected H atoms. Skipping. Residue SER 101 is missing expected H atoms. Skipping. Residue LEU 116 is missing expected H atoms. Skipping. Residue MET 319 is missing expected H atoms. Skipping. Residue LYS 323 is missing expected H atoms. Skipping. Residue THR 327 is missing expected H atoms. Skipping. Residue LYS 329 is missing expected H atoms. Skipping. Residue THR 371 is missing expected H atoms. Skipping. Residue LEU 377 is missing expected H atoms. Skipping. Residue ILE 421 is missing expected H atoms. Skipping. Residue LEU 427 is missing expected H atoms. Skipping. Residue VAL 490 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 107 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 PHE cc_start: 0.8864 (m-80) cc_final: 0.8558 (m-80) REVERT: A 45 THR cc_start: 0.9229 (m) cc_final: 0.8944 (p) REVERT: A 364 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8325 (tt) outliers start: 12 outliers final: 11 residues processed: 114 average time/residue: 0.2343 time to fit residues: 36.3035 Evaluate side-chains 116 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 GLU Chi-restraints excluded: chain A residue 52 SER Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 155 VAL Chi-restraints excluded: chain A residue 227 PHE Chi-restraints excluded: chain A residue 241 GLN Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 360 LEU Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 386 GLU Chi-restraints excluded: chain A residue 446 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.169086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145418 restraints weight = 18757.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.151228 restraints weight = 7132.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.154704 restraints weight = 3703.391| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.5740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4213 Z= 0.171 Angle : 0.520 4.934 5749 Z= 0.273 Chirality : 0.034 0.161 674 Planarity : 0.004 0.036 709 Dihedral : 4.807 36.485 620 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.83 % Allowed : 19.34 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.38), residues: 530 helix: 2.21 (0.27), residues: 368 sheet: None (None), residues: 0 loop : -0.92 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 64 HIS 0.002 0.001 HIS A 48 PHE 0.012 0.001 PHE A 275 TYR 0.021 0.002 TYR A 72 ARG 0.001 0.000 ARG A 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2952.95 seconds wall clock time: 52 minutes 51.96 seconds (3171.96 seconds total)