Starting phenix.real_space_refine on Sat Aug 23 21:58:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r22_18833/08_2025/8r22_18833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r22_18833/08_2025/8r22_18833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8r22_18833/08_2025/8r22_18833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r22_18833/08_2025/8r22_18833.map" model { file = "/net/cci-nas-00/data/ceres_data/8r22_18833/08_2025/8r22_18833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r22_18833/08_2025/8r22_18833.cif" } resolution = 3.9 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= 0.002 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 Zn 1 6.06 5 S 106 5.16 5 C 9620 2.51 5 N 2556 2.21 5 O 2786 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15069 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 5404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5404 Classifications: {'peptide': 710} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 41, 'TRANS': 667} Chain breaks: 8 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 3454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 451, 3454 Classifications: {'peptide': 451} Incomplete info: {'truncation_to_alanine': 25} Link IDs: {'PCIS': 4, 'PTRANS': 31, 'TRANS': 415} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 91 Unresolved non-hydrogen angles: 115 Unresolved non-hydrogen dihedrals: 80 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 42 Chain: "C" Number of atoms: 3447 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3447 Classifications: {'peptide': 436} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 416} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "D" Number of atoms: 2763 Number of conformers: 1 Conformer: "" Number of residues, atoms: 353, 2763 Classifications: {'peptide': 353} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 329} Chain breaks: 4 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N PRO A 492 " occ=0.25 ... (5 atoms not shown) pdb=" CD PRO A 492 " occ=0.25 Time building chain proxies: 3.34, per 1000 atoms: 0.22 Number of scatterers: 15069 At special positions: 0 Unit cell: (133.32, 124.08, 133.32, 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) Zn 1 29.99 S 106 16.00 O 2786 8.00 N 2556 7.00 C 9620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.18 Conformation dependent library (CDL) restraints added in 702.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C 800 " pdb="ZN ZN C 800 " - pdb=" ND1 HIS C 70 " pdb="ZN ZN C 800 " - pdb=" NE2 HIS C 68 " pdb="ZN ZN C 800 " - pdb=" NE2 HIS C 157 " 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3664 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 0 sheets defined 36.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 9 through 17 removed outlier: 3.994A pdb=" N VAL A 17 " --> pdb=" O CYS A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 39 Processing helix chain 'A' and resid 46 through 51 Processing helix chain 'A' and resid 55 through 61 Processing helix chain 'A' and resid 73 through 83 Processing helix chain 'A' and resid 87 through 92 Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 134 through 139 Processing helix chain 'A' and resid 146 through 152 Processing helix chain 'A' and resid 158 through 175 Processing helix chain 'A' and resid 193 through 205 Processing helix chain 'A' and resid 211 through 224 Processing helix chain 'A' and resid 231 through 247 removed outlier: 3.522A pdb=" N ALA A 235 " --> pdb=" O PRO A 231 " (cutoff:3.500A) Proline residue: A 242 - end of helix Processing helix chain 'A' and resid 258 through 267 Processing helix chain 'A' and resid 279 through 289 Processing helix chain 'A' and resid 295 through 303 Processing helix chain 'A' and resid 310 through 329 Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 349 through 356 Processing helix chain 'A' and resid 358 through 375 Processing helix chain 'A' and resid 388 through 402 Processing helix chain 'A' and resid 410 through 418 Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 443 through 457 Processing helix chain 'A' and resid 464 through 478 Processing helix chain 'A' and resid 494 through 508 Proline residue: A 503 - end of helix Processing helix chain 'A' and resid 514 through 530 Processing helix chain 'A' and resid 535 through 543 Processing helix chain 'A' and resid 546 through 552 Processing helix chain 'A' and resid 559 through 575 Processing helix chain 'A' and resid 590 through 601 removed outlier: 4.029A pdb=" N GLU A 595 " --> pdb=" O SER A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 621 Processing helix chain 'A' and resid 631 through 642 Processing helix chain 'A' and resid 650 through 665 Processing helix chain 'A' and resid 688 through 697 Processing helix chain 'A' and resid 700 through 708 Processing helix chain 'A' and resid 713 through 733 Processing helix chain 'A' and resid 769 through 778 Processing helix chain 'A' and resid 781 through 788 Processing helix chain 'A' and resid 799 through 808 Processing helix chain 'B' and resid 110 through 115 Processing helix chain 'B' and resid 127 through 145 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 184 through 192 Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 304 through 318 Processing helix chain 'B' and resid 333 through 341 Processing helix chain 'B' and resid 383 through 386 No H-bonds generated for 'chain 'B' and resid 383 through 386' Processing helix chain 'B' and resid 404 through 412 Processing helix chain 'B' and resid 429 through 433 Processing helix chain 'B' and resid 454 through 464 Processing helix chain 'C' and resid 57 through 60 No H-bonds generated for 'chain 'C' and resid 57 through 60' Processing helix chain 'C' and resid 77 through 78 No H-bonds generated for 'chain 'C' and resid 77 through 78' Processing helix chain 'C' and resid 94 through 113 Proline residue: C 101 - end of helix Processing helix chain 'C' and resid 123 through 130 Processing helix chain 'C' and resid 214 through 231 removed outlier: 3.502A pdb=" N ARG C 231 " --> pdb=" O GLU C 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 244 through 259 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 332 through 339 Processing helix chain 'C' and resid 359 through 363 Processing helix chain 'C' and resid 395 through 405 Processing helix chain 'C' and resid 420 through 431 removed outlier: 4.585A pdb=" N GLN C 425 " --> pdb=" O GLU C 421 " (cutoff:3.500A) Processing helix chain 'D' and resid 3 through 14 removed outlier: 3.896A pdb=" N ARG D 13 " --> pdb=" O VAL D 9 " (cutoff:3.500A) 438 hydrogen bonds defined for protein. 1314 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.49 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: 4906 1.34 - 1.46: 2973 1.46 - 1.58: 7381 1.58 - 1.69: 0 1.69 - 1.81: 151 Bond restraints: 15411 Sorted by residual: bond pdb=" C HIS B 246 " pdb=" N PRO B 247 " ideal model delta sigma weight residual 1.326 1.357 -0.030 1.44e-02 4.82e+03 4.47e+00 bond pdb=" C ASP D 339 " pdb=" N PRO D 340 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.87e+00 bond pdb=" CG PRO B 390 " pdb=" CD PRO B 390 " ideal model delta sigma weight residual 1.512 1.482 0.030 2.70e-02 1.37e+03 1.20e+00 bond pdb=" C GLY C 156 " pdb=" O GLY C 156 " ideal model delta sigma weight residual 1.237 1.231 0.006 7.00e-03 2.04e+04 8.33e-01 bond pdb=" CG LEU A 509 " pdb=" CD2 LEU A 509 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.32e-01 ... (remaining 15406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 20688 2.45 - 4.89: 252 4.89 - 7.34: 19 7.34 - 9.79: 1 9.79 - 12.23: 1 Bond angle restraints: 20961 Sorted by residual: angle pdb=" N THR C 324 " pdb=" CA THR C 324 " pdb=" C THR C 324 " ideal model delta sigma weight residual 109.30 116.38 -7.08 1.49e+00 4.50e-01 2.26e+01 angle pdb=" C ALA C 323 " pdb=" N THR C 324 " pdb=" CA THR C 324 " ideal model delta sigma weight residual 122.59 117.73 4.86 1.11e+00 8.12e-01 1.92e+01 angle pdb=" C ASP C 14 " pdb=" N VAL C 15 " pdb=" CA VAL C 15 " ideal model delta sigma weight residual 120.62 125.71 -5.09 1.64e+00 3.72e-01 9.61e+00 angle pdb=" C GLY B 396 " pdb=" N HIS B 397 " pdb=" CA HIS B 397 " ideal model delta sigma weight residual 120.69 111.57 9.12 2.95e+00 1.15e-01 9.56e+00 angle pdb=" C ALA B 109 " pdb=" N LEU B 110 " pdb=" CA LEU B 110 " ideal model delta sigma weight residual 119.78 123.27 -3.49 1.24e+00 6.50e-01 7.91e+00 ... (remaining 20956 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 8271 17.93 - 35.87: 797 35.87 - 53.80: 140 53.80 - 71.73: 24 71.73 - 89.67: 13 Dihedral angle restraints: 9245 sinusoidal: 3606 harmonic: 5639 Sorted by residual: dihedral pdb=" CA GLU C 301 " pdb=" C GLU C 301 " pdb=" N PHE C 302 " pdb=" CA PHE C 302 " ideal model delta harmonic sigma weight residual -180.00 -155.62 -24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" CA ALA A 255 " pdb=" C ALA A 255 " pdb=" N ALA A 256 " pdb=" CA ALA A 256 " ideal model delta harmonic sigma weight residual 180.00 156.61 23.39 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" CA SER B 223 " pdb=" C SER B 223 " pdb=" N ASN B 224 " pdb=" CA ASN B 224 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 9242 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1393 0.032 - 0.063: 701 0.063 - 0.095: 204 0.095 - 0.127: 101 0.127 - 0.158: 17 Chirality restraints: 2416 Sorted by residual: chirality pdb=" CA VAL C 144 " pdb=" N VAL C 144 " pdb=" C VAL C 144 " pdb=" CB VAL C 144 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA VAL D 300 " pdb=" N VAL D 300 " pdb=" C VAL D 300 " pdb=" CB VAL D 300 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.17e-01 chirality pdb=" CA ILE C 90 " pdb=" N ILE C 90 " pdb=" C ILE C 90 " pdb=" CB ILE C 90 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 2413 not shown) Planarity restraints: 2682 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 502 " -0.037 5.00e-02 4.00e+02 5.61e-02 5.04e+00 pdb=" N PRO A 503 " 0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 503 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 503 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 283 " 0.036 5.00e-02 4.00e+02 5.47e-02 4.79e+00 pdb=" N PRO C 284 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO C 284 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 284 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 105 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO A 106 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " 0.030 5.00e-02 4.00e+02 ... (remaining 2679 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 237 2.66 - 3.22: 14639 3.22 - 3.78: 22022 3.78 - 4.34: 29848 4.34 - 4.90: 49367 Nonbonded interactions: 116113 Sorted by model distance: nonbonded pdb=" OD2 ASP C 178 " pdb="ZN ZN C 800 " model vdw 2.098 2.230 nonbonded pdb=" OH TYR B 327 " pdb=" O ASP B 386 " model vdw 2.110 3.040 nonbonded pdb=" O LEU D 155 " pdb=" OG SER D 172 " model vdw 2.139 3.040 nonbonded pdb=" OE1 GLN D 301 " pdb=" OH TYR D 303 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR D 282 " pdb=" NE2 HIS D 347 " model vdw 2.177 3.120 ... (remaining 116108 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=0.25 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.040 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:0.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 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 : 0.005 0.232 15414 Z= 0.204 Angle : 0.673 12.234 20961 Z= 0.365 Chirality : 0.044 0.158 2416 Planarity : 0.005 0.056 2682 Dihedral : 14.653 89.667 5581 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -4.23 (0.16), residues: 1910 helix: -1.69 (0.16), residues: 793 sheet: -3.14 (0.26), residues: 263 loop : -3.82 (0.18), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 84 TYR 0.023 0.002 TYR C 278 PHE 0.029 0.002 PHE B 509 TRP 0.017 0.001 TRP D 7 HIS 0.005 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00417 (15411) covalent geometry : angle 0.67337 (20961) hydrogen bonds : bond 0.07280 ( 438) hydrogen bonds : angle 4.48733 ( 1314) metal coordination : bond 0.20474 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7851 (tt0) cc_final: 0.7478 (tm-30) REVERT: A 578 HIS cc_start: 0.7114 (m-70) cc_final: 0.6818 (m170) REVERT: A 657 LEU cc_start: 0.9093 (tp) cc_final: 0.8890 (tp) REVERT: A 781 LEU cc_start: 0.8420 (mm) cc_final: 0.8093 (mm) REVERT: B 93 LEU cc_start: 0.6701 (tp) cc_final: 0.6422 (tt) REVERT: B 184 MET cc_start: 0.7778 (mmm) cc_final: 0.7464 (mmm) REVERT: B 409 MET cc_start: 0.8914 (mtp) cc_final: 0.8689 (ttm) REVERT: C 30 MET cc_start: 0.8853 (ttm) cc_final: 0.8627 (ttm) REVERT: C 44 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7624 (ptt-90) REVERT: C 50 TYR cc_start: 0.6388 (m-80) cc_final: 0.6111 (m-80) REVERT: C 62 ASP cc_start: 0.7928 (m-30) cc_final: 0.7719 (m-30) REVERT: C 130 MET cc_start: 0.8573 (mmp) cc_final: 0.8348 (mmp) REVERT: C 378 LEU cc_start: 0.6495 (tp) cc_final: 0.6150 (tt) REVERT: D 211 PRO cc_start: 0.2871 (Cg_endo) cc_final: 0.2540 (Cg_exo) REVERT: D 362 ASN cc_start: 0.8364 (p0) cc_final: 0.7966 (p0) REVERT: D 363 ASP cc_start: 0.6189 (t0) cc_final: 0.5682 (t0) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1034 time to fit residues: 34.6643 Evaluate side-chains 155 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.0570 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 0.0570 overall best weight: 0.4016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 578 HIS A 653 GLN A 767 GLN B 15 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 GLN ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 334 ASN B 482 GLN C 13 GLN C 119 ASN C 124 GLN C 137 HIS C 198 ASN C 429 GLN ** D 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 112 GLN D 367 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.135960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.107933 restraints weight = 25684.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.106931 restraints weight = 33802.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108033 restraints weight = 38106.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109306 restraints weight = 22422.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.109828 restraints weight = 19346.755| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3356 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3356 r_free = 0.3356 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15414 Z= 0.112 Angle : 0.568 9.140 20961 Z= 0.287 Chirality : 0.042 0.145 2416 Planarity : 0.005 0.060 2682 Dihedral : 4.714 21.339 2063 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 1.09 % Allowed : 11.58 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.67 (0.18), residues: 1910 helix: -0.21 (0.18), residues: 803 sheet: -2.37 (0.28), residues: 263 loop : -3.19 (0.19), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 338 TYR 0.021 0.001 TYR C 107 PHE 0.019 0.001 PHE C 312 TRP 0.015 0.001 TRP D 283 HIS 0.006 0.001 HIS D 347 Details of bonding type rmsd covalent geometry : bond 0.00238 (15411) covalent geometry : angle 0.56806 (20961) hydrogen bonds : bond 0.03323 ( 438) hydrogen bonds : angle 3.78055 ( 1314) metal coordination : bond 0.01784 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7827 (tt0) cc_final: 0.7381 (tm-30) REVERT: A 454 LEU cc_start: 0.9173 (tp) cc_final: 0.8752 (tt) REVERT: A 724 LEU cc_start: 0.7080 (mt) cc_final: 0.6821 (mt) REVERT: B 32 MET cc_start: 0.7633 (mtm) cc_final: 0.7359 (mtm) REVERT: B 184 MET cc_start: 0.7826 (mmm) cc_final: 0.7558 (mmm) REVERT: B 206 PHE cc_start: 0.6164 (m-80) cc_final: 0.5891 (m-80) REVERT: B 500 ARG cc_start: 0.7233 (ttt180) cc_final: 0.7013 (ttt180) REVERT: C 56 ARG cc_start: 0.8183 (mtm-85) cc_final: 0.7973 (ptt90) REVERT: C 62 ASP cc_start: 0.7815 (m-30) cc_final: 0.7587 (m-30) REVERT: C 378 LEU cc_start: 0.6593 (tp) cc_final: 0.6251 (tt) REVERT: D 249 ARG cc_start: 0.6357 (ttt90) cc_final: 0.5986 (ptm-80) REVERT: D 362 ASN cc_start: 0.8371 (p0) cc_final: 0.7972 (p0) REVERT: D 363 ASP cc_start: 0.6123 (t0) cc_final: 0.5593 (t0) outliers start: 18 outliers final: 12 residues processed: 212 average time/residue: 0.0942 time to fit residues: 30.5791 Evaluate side-chains 172 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 367 HIS Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 120 optimal weight: 1.9990 chunk 148 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 96 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 179 optimal weight: 0.2980 chunk 145 optimal weight: 6.9990 chunk 157 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 92 optimal weight: 0.3980 chunk 4 optimal weight: 6.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN D 129 HIS D 367 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.135022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107451 restraints weight = 25644.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.105984 restraints weight = 38546.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.107269 restraints weight = 33336.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.109429 restraints weight = 23712.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109673 restraints weight = 20662.616| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3346 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3346 r_free = 0.3346 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3346 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15414 Z= 0.134 Angle : 0.573 8.647 20961 Z= 0.286 Chirality : 0.042 0.150 2416 Planarity : 0.005 0.055 2682 Dihedral : 4.542 20.791 2063 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.45 % Allowed : 13.99 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -2.11 (0.19), residues: 1910 helix: 0.33 (0.18), residues: 809 sheet: -1.99 (0.30), residues: 245 loop : -3.03 (0.19), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 56 TYR 0.025 0.001 TYR C 107 PHE 0.010 0.001 PHE B 509 TRP 0.022 0.001 TRP D 283 HIS 0.023 0.001 HIS D 129 Details of bonding type rmsd covalent geometry : bond 0.00321 (15411) covalent geometry : angle 0.57300 (20961) hydrogen bonds : bond 0.03427 ( 438) hydrogen bonds : angle 3.65212 ( 1314) metal coordination : bond 0.00421 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 264 LEU cc_start: 0.8757 (tp) cc_final: 0.8479 (mt) REVERT: A 373 GLU cc_start: 0.7847 (tt0) cc_final: 0.7335 (tm-30) REVERT: A 454 LEU cc_start: 0.9228 (tp) cc_final: 0.8832 (tt) REVERT: A 785 ARG cc_start: 0.6565 (ptm-80) cc_final: 0.6266 (mtp180) REVERT: B 27 ASP cc_start: 0.7018 (m-30) cc_final: 0.6674 (m-30) REVERT: B 32 MET cc_start: 0.7626 (mtm) cc_final: 0.7342 (mtm) REVERT: B 250 MET cc_start: 0.6873 (ttt) cc_final: 0.6672 (ttt) REVERT: B 486 MET cc_start: 0.7388 (mtm) cc_final: 0.6918 (tpt) REVERT: B 500 ARG cc_start: 0.7191 (ttt180) cc_final: 0.6951 (ttt180) REVERT: C 62 ASP cc_start: 0.7909 (m-30) cc_final: 0.7628 (m-30) REVERT: C 208 THR cc_start: 0.8721 (p) cc_final: 0.8327 (p) REVERT: C 378 LEU cc_start: 0.6473 (tp) cc_final: 0.6021 (tt) REVERT: D 249 ARG cc_start: 0.6358 (ttt90) cc_final: 0.6000 (ptm-80) REVERT: D 362 ASN cc_start: 0.8316 (p0) cc_final: 0.7898 (p0) REVERT: D 363 ASP cc_start: 0.6291 (t0) cc_final: 0.5769 (t0) outliers start: 24 outliers final: 14 residues processed: 193 average time/residue: 0.0941 time to fit residues: 27.3551 Evaluate side-chains 172 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 189 optimal weight: 0.8980 chunk 173 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 135 optimal weight: 0.0370 chunk 95 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 123 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.135963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.106877 restraints weight = 25451.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.105065 restraints weight = 35664.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.106055 restraints weight = 38028.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.108662 restraints weight = 24637.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109687 restraints weight = 17255.169| |-----------------------------------------------------------------------------| r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15414 Z= 0.111 Angle : 0.537 7.545 20961 Z= 0.267 Chirality : 0.041 0.149 2416 Planarity : 0.005 0.047 2682 Dihedral : 4.344 20.139 2063 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.11 % Allowed : 14.54 % Favored : 83.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -1.65 (0.19), residues: 1910 helix: 0.70 (0.19), residues: 809 sheet: -1.62 (0.31), residues: 245 loop : -2.81 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 211 TYR 0.020 0.001 TYR C 107 PHE 0.011 0.001 PHE B 509 TRP 0.025 0.001 TRP D 283 HIS 0.006 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00262 (15411) covalent geometry : angle 0.53665 (20961) hydrogen bonds : bond 0.03107 ( 438) hydrogen bonds : angle 3.49247 ( 1314) metal coordination : bond 0.00198 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.529 Fit side-chains REVERT: A 191 TRP cc_start: 0.7105 (m-10) cc_final: 0.6813 (m-10) REVERT: A 264 LEU cc_start: 0.8713 (tp) cc_final: 0.8484 (mp) REVERT: A 373 GLU cc_start: 0.7774 (tt0) cc_final: 0.7293 (tm-30) REVERT: A 454 LEU cc_start: 0.9145 (tp) cc_final: 0.8719 (tt) REVERT: B 27 ASP cc_start: 0.7040 (m-30) cc_final: 0.6720 (m-30) REVERT: B 93 LEU cc_start: 0.6126 (tt) cc_final: 0.5892 (tt) REVERT: B 250 MET cc_start: 0.6811 (ttt) cc_final: 0.6586 (ttt) REVERT: B 486 MET cc_start: 0.7348 (mtm) cc_final: 0.6884 (tpt) REVERT: B 500 ARG cc_start: 0.7141 (ttt180) cc_final: 0.6941 (ttt180) REVERT: C 5 ARG cc_start: 0.7352 (mtt90) cc_final: 0.7142 (mtm110) REVERT: C 30 MET cc_start: 0.8660 (ttm) cc_final: 0.8330 (ttt) REVERT: C 56 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7777 (ptt90) REVERT: C 62 ASP cc_start: 0.7846 (m-30) cc_final: 0.7612 (m-30) REVERT: C 208 THR cc_start: 0.8563 (p) cc_final: 0.8137 (p) REVERT: C 273 GLU cc_start: 0.5591 (OUTLIER) cc_final: 0.5308 (mp0) REVERT: C 278 TYR cc_start: 0.5577 (p90) cc_final: 0.4924 (p90) REVERT: C 378 LEU cc_start: 0.6310 (tp) cc_final: 0.5907 (tt) REVERT: D 214 ASN cc_start: 0.5727 (t0) cc_final: 0.5443 (t0) REVERT: D 249 ARG cc_start: 0.6335 (ttt90) cc_final: 0.6067 (ptm-80) REVERT: D 362 ASN cc_start: 0.8346 (p0) cc_final: 0.7914 (p0) REVERT: D 363 ASP cc_start: 0.6285 (t0) cc_final: 0.5764 (t0) outliers start: 35 outliers final: 22 residues processed: 209 average time/residue: 0.0930 time to fit residues: 29.5460 Evaluate side-chains 188 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 165 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 119 optimal weight: 0.8980 chunk 175 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 chunk 134 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 178 optimal weight: 2.9990 chunk 157 optimal weight: 0.6980 chunk 129 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 141 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 ASN D 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.136394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108428 restraints weight = 25483.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.106857 restraints weight = 39704.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.107921 restraints weight = 39132.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110184 restraints weight = 25790.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110433 restraints weight = 19419.938| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15414 Z= 0.104 Angle : 0.536 8.527 20961 Z= 0.264 Chirality : 0.041 0.146 2416 Planarity : 0.004 0.045 2682 Dihedral : 4.189 20.059 2063 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.29 % Allowed : 14.78 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -1.30 (0.20), residues: 1910 helix: 0.97 (0.19), residues: 811 sheet: -1.39 (0.32), residues: 255 loop : -2.63 (0.20), residues: 844 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 310 TYR 0.021 0.001 TYR C 107 PHE 0.013 0.001 PHE B 509 TRP 0.027 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00243 (15411) covalent geometry : angle 0.53627 (20961) hydrogen bonds : bond 0.02969 ( 438) hydrogen bonds : angle 3.41101 ( 1314) metal coordination : bond 0.00210 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 177 time to evaluate : 0.833 Fit side-chains REVERT: A 373 GLU cc_start: 0.7837 (tt0) cc_final: 0.7246 (tm-30) REVERT: A 454 LEU cc_start: 0.9107 (tp) cc_final: 0.8710 (tt) REVERT: B 27 ASP cc_start: 0.7072 (m-30) cc_final: 0.6744 (m-30) REVERT: B 486 MET cc_start: 0.7338 (mtm) cc_final: 0.6943 (tpt) REVERT: B 500 ARG cc_start: 0.7121 (ttt180) cc_final: 0.6880 (ttt180) REVERT: C 5 ARG cc_start: 0.7315 (mtt90) cc_final: 0.7096 (mtm110) REVERT: C 30 MET cc_start: 0.8681 (ttm) cc_final: 0.8378 (ttt) REVERT: C 56 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7840 (ptt90) REVERT: C 62 ASP cc_start: 0.7810 (m-30) cc_final: 0.7578 (m-30) REVERT: C 208 THR cc_start: 0.8469 (p) cc_final: 0.8086 (p) REVERT: C 259 MET cc_start: 0.7623 (mmm) cc_final: 0.7394 (mmm) REVERT: C 273 GLU cc_start: 0.5518 (OUTLIER) cc_final: 0.5257 (mp0) REVERT: C 278 TYR cc_start: 0.5577 (p90) cc_final: 0.4916 (p90) REVERT: D 207 GLN cc_start: 0.6755 (tm-30) cc_final: 0.6441 (tm-30) REVERT: D 214 ASN cc_start: 0.5833 (t0) cc_final: 0.5616 (t0) REVERT: D 249 ARG cc_start: 0.6425 (ttt90) cc_final: 0.6042 (ptm-80) REVERT: D 362 ASN cc_start: 0.8318 (p0) cc_final: 0.7895 (p0) REVERT: D 363 ASP cc_start: 0.6299 (t0) cc_final: 0.5758 (t0) outliers start: 38 outliers final: 26 residues processed: 205 average time/residue: 0.0922 time to fit residues: 28.5410 Evaluate side-chains 187 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 160 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 176 ASP Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 76 optimal weight: 0.8980 chunk 90 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 145 optimal weight: 3.9990 chunk 151 optimal weight: 5.9990 chunk 108 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 68 optimal weight: 0.5980 chunk 112 optimal weight: 5.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.137480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108638 restraints weight = 25073.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107646 restraints weight = 33933.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.109155 restraints weight = 36031.512| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110940 restraints weight = 21236.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.111285 restraints weight = 18453.691| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15414 Z= 0.110 Angle : 0.537 7.242 20961 Z= 0.264 Chirality : 0.041 0.147 2416 Planarity : 0.004 0.044 2682 Dihedral : 4.114 19.600 2063 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 2.11 % Allowed : 15.56 % Favored : 82.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -1.10 (0.20), residues: 1910 helix: 1.12 (0.19), residues: 812 sheet: -1.24 (0.32), residues: 255 loop : -2.52 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 177 TYR 0.021 0.001 TYR C 107 PHE 0.014 0.001 PHE C 312 TRP 0.029 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00260 (15411) covalent geometry : angle 0.53738 (20961) hydrogen bonds : bond 0.02931 ( 438) hydrogen bonds : angle 3.36767 ( 1314) metal coordination : bond 0.00195 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 0.387 Fit side-chains REVERT: A 373 GLU cc_start: 0.7842 (tt0) cc_final: 0.7308 (tm-30) REVERT: A 454 LEU cc_start: 0.9114 (tp) cc_final: 0.8722 (tt) REVERT: B 27 ASP cc_start: 0.7090 (m-30) cc_final: 0.6764 (m-30) REVERT: B 486 MET cc_start: 0.7544 (mtm) cc_final: 0.7015 (tpt) REVERT: B 500 ARG cc_start: 0.7177 (ttt180) cc_final: 0.6951 (ttt-90) REVERT: C 5 ARG cc_start: 0.7403 (mtt90) cc_final: 0.7185 (mtm110) REVERT: C 62 ASP cc_start: 0.7795 (m-30) cc_final: 0.7536 (m-30) REVERT: C 208 THR cc_start: 0.8540 (p) cc_final: 0.8145 (p) REVERT: C 231 ARG cc_start: 0.7814 (ttt90) cc_final: 0.7483 (ttt180) REVERT: C 259 MET cc_start: 0.7782 (mmm) cc_final: 0.7512 (mmm) REVERT: C 273 GLU cc_start: 0.5460 (OUTLIER) cc_final: 0.5152 (mp0) REVERT: C 278 TYR cc_start: 0.5556 (p90) cc_final: 0.4888 (p90) REVERT: D 214 ASN cc_start: 0.5882 (t0) cc_final: 0.5639 (t0) REVERT: D 249 ARG cc_start: 0.6354 (ttt90) cc_final: 0.5928 (ptm-80) REVERT: D 362 ASN cc_start: 0.8335 (p0) cc_final: 0.7907 (p0) REVERT: D 363 ASP cc_start: 0.6280 (t0) cc_final: 0.5726 (t0) outliers start: 35 outliers final: 30 residues processed: 200 average time/residue: 0.0902 time to fit residues: 27.3804 Evaluate side-chains 193 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 162 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 161 VAL Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 104 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 112 optimal weight: 5.9990 chunk 30 optimal weight: 0.0020 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 207 GLN D 214 ASN D 367 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.110398 restraints weight = 25016.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.110234 restraints weight = 36919.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.111523 restraints weight = 36015.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.112636 restraints weight = 22042.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.113203 restraints weight = 19276.303| |-----------------------------------------------------------------------------| r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15414 Z= 0.101 Angle : 0.526 7.568 20961 Z= 0.259 Chirality : 0.041 0.149 2416 Planarity : 0.004 0.043 2682 Dihedral : 4.017 19.782 2063 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.17 % Allowed : 15.98 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -0.89 (0.20), residues: 1910 helix: 1.28 (0.19), residues: 812 sheet: -1.07 (0.33), residues: 255 loop : -2.43 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 56 TYR 0.020 0.001 TYR C 107 PHE 0.008 0.001 PHE A 159 TRP 0.032 0.001 TRP D 283 HIS 0.006 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00236 (15411) covalent geometry : angle 0.52640 (20961) hydrogen bonds : bond 0.02807 ( 438) hydrogen bonds : angle 3.31601 ( 1314) metal coordination : bond 0.00176 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 172 time to evaluate : 0.576 Fit side-chains REVERT: A 373 GLU cc_start: 0.7857 (tt0) cc_final: 0.7300 (tm-30) REVERT: A 454 LEU cc_start: 0.9098 (tp) cc_final: 0.8688 (tt) REVERT: A 806 MET cc_start: 0.8271 (tpp) cc_final: 0.8049 (tpp) REVERT: B 27 ASP cc_start: 0.7085 (m-30) cc_final: 0.6773 (m-30) REVERT: B 93 LEU cc_start: 0.6050 (OUTLIER) cc_final: 0.5699 (tt) REVERT: B 204 GLU cc_start: 0.7589 (mp0) cc_final: 0.6784 (mt-10) REVERT: B 486 MET cc_start: 0.7508 (mtm) cc_final: 0.6978 (tpt) REVERT: B 500 ARG cc_start: 0.7144 (ttt180) cc_final: 0.6903 (ttt-90) REVERT: C 56 ARG cc_start: 0.7988 (mtm-85) cc_final: 0.7677 (ptt90) REVERT: C 62 ASP cc_start: 0.7722 (m-30) cc_final: 0.7486 (m-30) REVERT: C 208 THR cc_start: 0.8663 (p) cc_final: 0.8324 (p) REVERT: C 231 ARG cc_start: 0.7754 (ttt90) cc_final: 0.7425 (ttt180) REVERT: C 259 MET cc_start: 0.8041 (mmm) cc_final: 0.7839 (mmm) REVERT: C 273 GLU cc_start: 0.5183 (OUTLIER) cc_final: 0.4939 (mp0) REVERT: C 278 TYR cc_start: 0.5574 (p90) cc_final: 0.4893 (p90) REVERT: C 310 ARG cc_start: 0.6863 (ttp80) cc_final: 0.6636 (ttp80) REVERT: D 214 ASN cc_start: 0.5992 (OUTLIER) cc_final: 0.5791 (t0) REVERT: D 249 ARG cc_start: 0.6377 (ttt90) cc_final: 0.6017 (ptm-80) REVERT: D 362 ASN cc_start: 0.8298 (p0) cc_final: 0.7862 (p0) REVERT: D 363 ASP cc_start: 0.6212 (t0) cc_final: 0.5670 (t0) outliers start: 36 outliers final: 28 residues processed: 199 average time/residue: 0.0996 time to fit residues: 29.5861 Evaluate side-chains 189 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 158 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 214 ASN Chi-restraints excluded: chain D residue 291 LEU Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 167 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 55 optimal weight: 0.8980 chunk 174 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 169 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 112 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 ASN D 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110206 restraints weight = 25097.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111193 restraints weight = 34612.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111952 restraints weight = 32211.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.114376 restraints weight = 21219.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.114559 restraints weight = 15533.977| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 15414 Z= 0.101 Angle : 0.536 7.663 20961 Z= 0.263 Chirality : 0.041 0.146 2416 Planarity : 0.004 0.042 2682 Dihedral : 3.958 19.498 2063 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.93 % Allowed : 16.59 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -0.82 (0.20), residues: 1910 helix: 1.37 (0.19), residues: 811 sheet: -1.17 (0.33), residues: 254 loop : -2.35 (0.21), residues: 845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 56 TYR 0.028 0.001 TYR C 107 PHE 0.008 0.001 PHE B 509 TRP 0.028 0.001 TRP D 283 HIS 0.006 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00237 (15411) covalent geometry : angle 0.53611 (20961) hydrogen bonds : bond 0.02769 ( 438) hydrogen bonds : angle 3.27897 ( 1314) metal coordination : bond 0.00204 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.564 Fit side-chains REVERT: A 7 GLN cc_start: 0.7690 (mp10) cc_final: 0.7461 (mm-40) REVERT: A 373 GLU cc_start: 0.7867 (tt0) cc_final: 0.7221 (tm-30) REVERT: A 454 LEU cc_start: 0.9090 (tp) cc_final: 0.8679 (tt) REVERT: A 806 MET cc_start: 0.8253 (tpp) cc_final: 0.7982 (tpp) REVERT: B 27 ASP cc_start: 0.7120 (m-30) cc_final: 0.6807 (m-30) REVERT: B 93 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5703 (tt) REVERT: B 204 GLU cc_start: 0.7566 (mp0) cc_final: 0.6777 (mt-10) REVERT: B 486 MET cc_start: 0.7546 (mtm) cc_final: 0.6754 (tpt) REVERT: B 500 ARG cc_start: 0.7142 (ttt180) cc_final: 0.6904 (ttt-90) REVERT: C 35 MET cc_start: 0.8431 (ttt) cc_final: 0.7969 (ttt) REVERT: C 56 ARG cc_start: 0.7996 (mtm-85) cc_final: 0.7659 (ptt90) REVERT: C 62 ASP cc_start: 0.7668 (m-30) cc_final: 0.7454 (m-30) REVERT: C 208 THR cc_start: 0.8656 (p) cc_final: 0.8315 (p) REVERT: C 273 GLU cc_start: 0.5146 (OUTLIER) cc_final: 0.4893 (mp0) REVERT: C 278 TYR cc_start: 0.5581 (p90) cc_final: 0.4897 (p90) REVERT: D 214 ASN cc_start: 0.5385 (t0) cc_final: 0.5181 (t0) REVERT: D 249 ARG cc_start: 0.6414 (ttt90) cc_final: 0.6091 (ptm-80) REVERT: D 291 LEU cc_start: 0.6639 (pt) cc_final: 0.6395 (tt) REVERT: D 362 ASN cc_start: 0.8291 (p0) cc_final: 0.7849 (p0) REVERT: D 363 ASP cc_start: 0.6177 (t0) cc_final: 0.5627 (t0) outliers start: 32 outliers final: 27 residues processed: 190 average time/residue: 0.1016 time to fit residues: 28.9731 Evaluate side-chains 186 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 168 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 160 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 165 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 189 optimal weight: 9.9990 chunk 77 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN D 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.138356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110486 restraints weight = 25065.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109153 restraints weight = 34863.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.110149 restraints weight = 38264.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.112516 restraints weight = 24326.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.113057 restraints weight = 17295.068| |-----------------------------------------------------------------------------| r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15414 Z= 0.105 Angle : 0.549 11.886 20961 Z= 0.267 Chirality : 0.041 0.147 2416 Planarity : 0.004 0.042 2682 Dihedral : 3.918 19.161 2063 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.99 % Allowed : 17.19 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -0.71 (0.20), residues: 1910 helix: 1.43 (0.19), residues: 807 sheet: -1.26 (0.32), residues: 269 loop : -2.20 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 17 TYR 0.023 0.001 TYR C 107 PHE 0.009 0.001 PHE B 509 TRP 0.030 0.001 TRP D 283 HIS 0.006 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00247 (15411) covalent geometry : angle 0.54916 (20961) hydrogen bonds : bond 0.02839 ( 438) hydrogen bonds : angle 3.32364 ( 1314) metal coordination : bond 0.00212 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.451 Fit side-chains REVERT: A 7 GLN cc_start: 0.7652 (mp10) cc_final: 0.7402 (mm-40) REVERT: A 373 GLU cc_start: 0.7861 (tt0) cc_final: 0.7275 (tm-30) REVERT: A 454 LEU cc_start: 0.9111 (tp) cc_final: 0.8706 (tt) REVERT: A 591 SER cc_start: 0.8236 (t) cc_final: 0.7786 (p) REVERT: A 806 MET cc_start: 0.8346 (tpp) cc_final: 0.8049 (tpp) REVERT: B 27 ASP cc_start: 0.7172 (m-30) cc_final: 0.6839 (m-30) REVERT: B 93 LEU cc_start: 0.6065 (OUTLIER) cc_final: 0.5736 (tt) REVERT: B 184 MET cc_start: 0.7835 (mmp) cc_final: 0.7590 (mmp) REVERT: B 204 GLU cc_start: 0.7599 (mp0) cc_final: 0.6796 (mt-10) REVERT: B 500 ARG cc_start: 0.7102 (ttt180) cc_final: 0.6872 (ttt180) REVERT: C 35 MET cc_start: 0.8409 (ttt) cc_final: 0.8159 (ttt) REVERT: C 62 ASP cc_start: 0.7678 (m-30) cc_final: 0.7459 (m-30) REVERT: C 208 THR cc_start: 0.8645 (p) cc_final: 0.8321 (p) REVERT: C 273 GLU cc_start: 0.5258 (OUTLIER) cc_final: 0.5021 (mp0) REVERT: C 278 TYR cc_start: 0.5515 (p90) cc_final: 0.4714 (p90) REVERT: D 249 ARG cc_start: 0.6436 (ttt90) cc_final: 0.6059 (ptm-80) REVERT: D 291 LEU cc_start: 0.6723 (pt) cc_final: 0.6480 (tt) REVERT: D 362 ASN cc_start: 0.8292 (p0) cc_final: 0.7870 (p0) REVERT: D 363 ASP cc_start: 0.6258 (t0) cc_final: 0.5675 (t0) outliers start: 33 outliers final: 29 residues processed: 193 average time/residue: 0.1044 time to fit residues: 30.6102 Evaluate side-chains 192 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 51 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 103 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 19 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 107 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 184 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN ** C 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 367 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.136599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.107890 restraints weight = 25458.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107718 restraints weight = 40410.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.108712 restraints weight = 37226.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111546 restraints weight = 24552.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.112162 restraints weight = 16880.444| |-----------------------------------------------------------------------------| r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15414 Z= 0.143 Angle : 0.577 10.214 20961 Z= 0.284 Chirality : 0.042 0.168 2416 Planarity : 0.004 0.042 2682 Dihedral : 4.063 19.987 2063 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 1.93 % Allowed : 17.31 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -0.82 (0.20), residues: 1910 helix: 1.32 (0.19), residues: 808 sheet: -1.45 (0.31), residues: 289 loop : -2.18 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 310 TYR 0.027 0.001 TYR C 107 PHE 0.011 0.001 PHE B 281 TRP 0.037 0.001 TRP D 283 HIS 0.006 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00344 (15411) covalent geometry : angle 0.57730 (20961) hydrogen bonds : bond 0.03240 ( 438) hydrogen bonds : angle 3.45859 ( 1314) metal coordination : bond 0.00338 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3820 Ramachandran restraints generated. 1910 Oldfield, 0 Emsley, 1910 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 164 time to evaluate : 0.540 Fit side-chains REVERT: A 7 GLN cc_start: 0.7629 (mp10) cc_final: 0.7375 (mm-40) REVERT: A 373 GLU cc_start: 0.7918 (tt0) cc_final: 0.7336 (tm-30) REVERT: A 454 LEU cc_start: 0.9210 (tp) cc_final: 0.8852 (tt) REVERT: A 806 MET cc_start: 0.8349 (tpp) cc_final: 0.8052 (tpp) REVERT: B 27 ASP cc_start: 0.7258 (m-30) cc_final: 0.6933 (m-30) REVERT: B 93 LEU cc_start: 0.6085 (OUTLIER) cc_final: 0.5782 (tt) REVERT: B 204 GLU cc_start: 0.7660 (mp0) cc_final: 0.6790 (mt-10) REVERT: B 500 ARG cc_start: 0.7132 (ttt180) cc_final: 0.6889 (ttt180) REVERT: C 62 ASP cc_start: 0.7811 (m-30) cc_final: 0.7538 (m-30) REVERT: C 208 THR cc_start: 0.8654 (p) cc_final: 0.8337 (p) REVERT: C 273 GLU cc_start: 0.5308 (OUTLIER) cc_final: 0.5038 (mp0) REVERT: C 278 TYR cc_start: 0.5572 (p90) cc_final: 0.4738 (p90) REVERT: C 327 MET cc_start: 0.7445 (ptp) cc_final: 0.7162 (ptp) REVERT: D 249 ARG cc_start: 0.6483 (ttt90) cc_final: 0.6128 (ptm-80) REVERT: D 291 LEU cc_start: 0.6740 (pt) cc_final: 0.6472 (tt) REVERT: D 362 ASN cc_start: 0.8304 (p0) cc_final: 0.7894 (p0) REVERT: D 363 ASP cc_start: 0.6170 (t0) cc_final: 0.5538 (t0) outliers start: 32 outliers final: 29 residues processed: 190 average time/residue: 0.1013 time to fit residues: 29.4502 Evaluate side-chains 191 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 160 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 143 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 720 CYS Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 51 ILE Chi-restraints excluded: chain C residue 149 GLU Chi-restraints excluded: chain C residue 150 ILE Chi-restraints excluded: chain C residue 157 HIS Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain C residue 205 THR Chi-restraints excluded: chain C residue 216 CYS Chi-restraints excluded: chain C residue 269 THR Chi-restraints excluded: chain C residue 273 GLU Chi-restraints excluded: chain C residue 302 PHE Chi-restraints excluded: chain C residue 314 ASP Chi-restraints excluded: chain C residue 355 VAL Chi-restraints excluded: chain C residue 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 141 VAL Chi-restraints excluded: chain D residue 151 HIS Chi-restraints excluded: chain D residue 174 VAL Chi-restraints excluded: chain D residue 344 VAL Chi-restraints excluded: chain D residue 368 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 183 optimal weight: 50.0000 chunk 73 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 185 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 ASN C 335 GLN D 367 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.136922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108411 restraints weight = 25205.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.107020 restraints weight = 37080.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.108083 restraints weight = 38200.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.110698 restraints weight = 24264.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.111557 restraints weight = 16968.916| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15414 Z= 0.132 Angle : 0.575 11.640 20961 Z= 0.281 Chirality : 0.042 0.181 2416 Planarity : 0.004 0.041 2682 Dihedral : 4.058 20.226 2063 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.11 % Allowed : 17.25 % Favored : 80.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % 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 aren not related in a simple way. whole: -0.79 (0.20), residues: 1910 helix: 1.31 (0.19), residues: 809 sheet: -1.30 (0.32), residues: 277 loop : -2.19 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 310 TYR 0.029 0.001 TYR C 107 PHE 0.017 0.001 PHE A 705 TRP 0.042 0.001 TRP D 283 HIS 0.006 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00316 (15411) covalent geometry : angle 0.57532 (20961) hydrogen bonds : bond 0.03219 ( 438) hydrogen bonds : angle 3.47776 ( 1314) metal coordination : bond 0.00291 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1716.01 seconds wall clock time: 30 minutes 36.63 seconds (1836.63 seconds total)