Starting phenix.real_space_refine on Fri May 16 22:55:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r22_18833/05_2025/8r22_18833.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r22_18833/05_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_18833/05_2025/8r22_18833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r22_18833/05_2025/8r22_18833.map" model { file = "/net/cci-nas-00/data/ceres_data/8r22_18833/05_2025/8r22_18833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r22_18833/05_2025/8r22_18833.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'HIS: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: {'HIS:plan': 1, 'ARG:plan': 1, 'ASP: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: 9.13, per 1000 atoms: 0.61 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: 3.06 Conformation dependent library (CDL) restraints added in 1.8 seconds 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: 1.09 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: 3.31 Time building geometry restraints manager: 3.60 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: 0.720 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 34.050 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.050 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: 0.010 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.23 (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 TRP 0.017 0.001 TRP D 7 HIS 0.005 0.001 HIS D 347 PHE 0.029 0.002 PHE B 509 TYR 0.023 0.002 TYR C 278 ARG 0.004 0.000 ARG D 84 Details of bonding type rmsd hydrogen bonds : bond 0.07280 ( 438) hydrogen bonds : angle 4.48733 ( 1314) metal coordination : bond 0.20474 ( 3) covalent geometry : bond 0.00417 (15411) covalent geometry : angle 0.67337 (20961) *********************** 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 : 1.859 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: 0.8092 (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: 0.7466 (mmm) REVERT: B 409 MET cc_start: 0.8914 (mtp) cc_final: 0.8690 (ttm) REVERT: C 30 MET cc_start: 0.8853 (ttm) cc_final: 0.8626 (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: 0.6109 (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: 0.8349 (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: 0.2541 (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: 0.5683 (t0) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.2700 time to fit residues: 90.0054 Evaluate side-chains 156 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 163 optimal weight: 8.9990 chunk 147 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 152 optimal weight: 7.9990 chunk 58 optimal weight: 0.9990 chunk 92 optimal weight: 6.9990 chunk 113 optimal weight: 0.9990 chunk 176 optimal weight: 10.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 201 HIS 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 482 GLN C 13 GLN C 119 ASN C 124 GLN C 137 HIS C 198 ASN C 429 GLN ** 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 = 0.3703 r_free = 0.3703 target = 0.134662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.107818 restraints weight = 25741.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.107735 restraints weight = 37409.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108409 restraints weight = 36845.960| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3344 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3344 r_free = 0.3344 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.1087 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= 0.127 Angle : 0.587 9.751 20961 Z= 0.295 Chirality : 0.043 0.147 2416 Planarity : 0.005 0.062 2682 Dihedral : 4.838 21.457 2063 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 1.21 % Allowed : 12.06 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.81 (0.18), residues: 1910 helix: -0.30 (0.18), residues: 801 sheet: -2.47 (0.27), residues: 273 loop : -3.27 (0.19), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP D 283 HIS 0.006 0.001 HIS D 347 PHE 0.021 0.001 PHE C 312 TYR 0.023 0.001 TYR C 107 ARG 0.004 0.000 ARG A 562 Details of bonding type rmsd hydrogen bonds : bond 0.03612 ( 438) hydrogen bonds : angle 3.90221 ( 1314) metal coordination : bond 0.00730 ( 3) covalent geometry : bond 0.00294 (15411) covalent geometry : angle 0.58702 (20961) *********************** 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 208 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 188 time to evaluate : 1.599 Fit side-chains revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7907 (tt0) cc_final: 0.7394 (tm-30) REVERT: B 32 MET cc_start: 0.7611 (mtm) cc_final: 0.7327 (mtm) REVERT: B 206 PHE cc_start: 0.6077 (m-80) cc_final: 0.5811 (m-80) REVERT: C 30 MET cc_start: 0.8774 (ttm) cc_final: 0.8555 (ttm) REVERT: C 50 TYR cc_start: 0.6342 (m-80) cc_final: 0.6124 (m-80) REVERT: C 56 ARG cc_start: 0.8310 (mtm-85) cc_final: 0.8097 (ptt90) REVERT: C 62 ASP cc_start: 0.7963 (m-30) cc_final: 0.7707 (m-30) REVERT: C 265 ILE cc_start: 0.9067 (mm) cc_final: 0.8854 (mt) REVERT: C 378 LEU cc_start: 0.6712 (tp) cc_final: 0.6349 (tt) REVERT: C 382 MET cc_start: 0.8738 (ptm) cc_final: 0.8535 (ptp) REVERT: D 202 LEU cc_start: 0.6231 (OUTLIER) cc_final: 0.5937 (mt) REVERT: D 249 ARG cc_start: 0.6349 (ttt90) cc_final: 0.6013 (ptm-80) REVERT: D 362 ASN cc_start: 0.8356 (p0) cc_final: 0.7953 (p0) REVERT: D 363 ASP cc_start: 0.6266 (t0) cc_final: 0.5738 (t0) outliers start: 20 outliers final: 12 residues processed: 202 average time/residue: 0.2309 time to fit residues: 71.8374 Evaluate side-chains 166 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 153 time to evaluate : 1.552 ------------------------------------------------------------------------------- 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 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 176 ASP Chi-restraints excluded: chain D residue 202 LEU 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 160 optimal weight: 5.9990 chunk 188 optimal weight: 5.9990 chunk 122 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 185 optimal weight: 0.0040 chunk 172 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 77 optimal weight: 0.9990 chunk 189 optimal weight: 20.0000 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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** B 334 ASN C 119 ASN D 49 ASN D 367 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.135778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.108204 restraints weight = 25218.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106432 restraints weight = 37330.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107613 restraints weight = 38785.556| |-----------------------------------------------------------------------------| r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.97 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15414 Z= 0.117 Angle : 0.558 8.433 20961 Z= 0.279 Chirality : 0.041 0.156 2416 Planarity : 0.005 0.056 2682 Dihedral : 4.534 20.867 2063 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 1.33 % Allowed : 14.35 % Favored : 84.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.19), residues: 1910 helix: 0.39 (0.18), residues: 807 sheet: -2.00 (0.29), residues: 249 loop : -2.99 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP D 283 HIS 0.004 0.001 HIS D 347 PHE 0.014 0.001 PHE B 509 TYR 0.018 0.001 TYR C 107 ARG 0.004 0.000 ARG A 610 Details of bonding type rmsd hydrogen bonds : bond 0.03209 ( 438) hydrogen bonds : angle 3.60672 ( 1314) metal coordination : bond 0.00265 ( 3) covalent geometry : bond 0.00262 (15411) covalent geometry : angle 0.55775 (20961) *********************** 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 200 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 1.703 Fit side-chains REVERT: A 373 GLU cc_start: 0.7831 (tt0) cc_final: 0.7312 (tm-30) REVERT: A 454 LEU cc_start: 0.9181 (tp) cc_final: 0.8773 (tt) REVERT: B 27 ASP cc_start: 0.7040 (m-30) cc_final: 0.6713 (m-30) REVERT: B 32 MET cc_start: 0.7631 (mtm) cc_final: 0.7315 (mtm) REVERT: B 287 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8616 (tp) REVERT: B 486 MET cc_start: 0.7414 (mtm) cc_final: 0.6941 (tpt) REVERT: B 500 ARG cc_start: 0.7201 (ttt180) cc_final: 0.6952 (ttt180) REVERT: C 56 ARG cc_start: 0.8241 (mtm-85) cc_final: 0.8024 (ptt90) REVERT: C 62 ASP cc_start: 0.7850 (m-30) cc_final: 0.7607 (m-30) REVERT: C 208 THR cc_start: 0.8599 (p) cc_final: 0.8200 (p) REVERT: C 378 LEU cc_start: 0.6607 (tp) cc_final: 0.6215 (tt) REVERT: D 202 LEU cc_start: 0.6249 (mt) cc_final: 0.6032 (mt) REVERT: D 214 ASN cc_start: 0.5443 (t0) cc_final: 0.5216 (t0) REVERT: D 241 ILE cc_start: 0.7554 (mp) cc_final: 0.7196 (mp) REVERT: D 249 ARG cc_start: 0.6324 (ttt90) cc_final: 0.6115 (ptm-80) REVERT: D 362 ASN cc_start: 0.8345 (p0) cc_final: 0.7946 (p0) REVERT: D 363 ASP cc_start: 0.6314 (t0) cc_final: 0.5776 (t0) outliers start: 22 outliers final: 14 residues processed: 193 average time/residue: 0.2542 time to fit residues: 73.9987 Evaluate side-chains 170 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 155 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 294 HIS Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 688 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 287 LEU 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 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 132 optimal weight: 4.9990 chunk 189 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 119 optimal weight: 0.2980 chunk 168 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 49 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 = 0.3716 r_free = 0.3716 target = 0.136020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108011 restraints weight = 25313.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.107043 restraints weight = 38152.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.108354 restraints weight = 32147.964| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1780 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= 0.113 Angle : 0.536 7.593 20961 Z= 0.267 Chirality : 0.041 0.145 2416 Planarity : 0.004 0.046 2682 Dihedral : 4.331 20.099 2063 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.19), residues: 1910 helix: 0.76 (0.19), residues: 811 sheet: -1.57 (0.31), residues: 245 loop : -2.81 (0.20), residues: 854 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.013 0.001 PHE B 509 TYR 0.023 0.001 TYR C 107 ARG 0.003 0.000 ARG A 285 Details of bonding type rmsd hydrogen bonds : bond 0.03122 ( 438) hydrogen bonds : angle 3.48138 ( 1314) metal coordination : bond 0.00286 ( 3) covalent geometry : bond 0.00266 (15411) covalent geometry : angle 0.53647 (20961) *********************** 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 218 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 1.576 Fit side-chains REVERT: A 373 GLU cc_start: 0.7791 (tt0) cc_final: 0.7259 (tm-30) REVERT: A 454 LEU cc_start: 0.9186 (tp) cc_final: 0.8786 (tt) REVERT: B 27 ASP cc_start: 0.7077 (m-30) cc_final: 0.6785 (m-30) REVERT: B 93 LEU cc_start: 0.6069 (tt) cc_final: 0.5792 (tt) REVERT: B 287 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8702 (tp) REVERT: B 486 MET cc_start: 0.7395 (mtm) cc_final: 0.6913 (tpt) REVERT: B 500 ARG cc_start: 0.7171 (ttt180) cc_final: 0.6968 (ttt180) REVERT: C 5 ARG cc_start: 0.7310 (mtt90) cc_final: 0.7074 (mtm110) REVERT: C 62 ASP cc_start: 0.7791 (m-30) cc_final: 0.7526 (m-30) REVERT: C 208 THR cc_start: 0.8613 (p) cc_final: 0.8202 (p) REVERT: C 273 GLU cc_start: 0.5582 (OUTLIER) cc_final: 0.5290 (mp0) REVERT: C 278 TYR cc_start: 0.5601 (p90) cc_final: 0.4946 (p90) REVERT: C 378 LEU cc_start: 0.6376 (tp) cc_final: 0.5977 (tt) REVERT: D 202 LEU cc_start: 0.6091 (OUTLIER) cc_final: 0.5825 (mt) REVERT: D 241 ILE cc_start: 0.7382 (mp) cc_final: 0.7060 (mp) REVERT: D 249 ARG cc_start: 0.6345 (ttt90) cc_final: 0.5970 (ptm-80) REVERT: D 362 ASN cc_start: 0.8322 (p0) cc_final: 0.7896 (p0) REVERT: D 363 ASP cc_start: 0.6366 (t0) cc_final: 0.5857 (t0) outliers start: 38 outliers final: 22 residues processed: 212 average time/residue: 0.2542 time to fit residues: 81.1607 Evaluate side-chains 191 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 1.832 ------------------------------------------------------------------------------- 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 B residue 287 LEU 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 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 434 ASN Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 49 ASN Chi-restraints excluded: chain D residue 118 ASP 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 202 LEU 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 191 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 121 optimal weight: 0.7980 chunk 125 optimal weight: 0.6980 chunk 145 optimal weight: 5.9990 chunk 135 optimal weight: 0.1980 chunk 88 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 122 optimal weight: 0.9990 chunk 50 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.136465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.108545 restraints weight = 25478.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107451 restraints weight = 38924.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.108654 restraints weight = 33788.990| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.1945 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= 0.102 Angle : 0.534 8.045 20961 Z= 0.263 Chirality : 0.041 0.145 2416 Planarity : 0.004 0.045 2682 Dihedral : 4.223 19.876 2063 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.05 % Allowed : 15.80 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.19), residues: 1910 helix: 0.98 (0.19), residues: 811 sheet: -1.39 (0.31), residues: 256 loop : -2.66 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 283 HIS 0.008 0.001 HIS C 157 PHE 0.013 0.001 PHE B 509 TYR 0.029 0.001 TYR C 107 ARG 0.004 0.000 ARG C 56 Details of bonding type rmsd hydrogen bonds : bond 0.02953 ( 438) hydrogen bonds : angle 3.38984 ( 1314) metal coordination : bond 0.00184 ( 3) covalent geometry : bond 0.00238 (15411) covalent geometry : angle 0.53426 (20961) *********************** 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 211 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 1.622 Fit side-chains REVERT: A 373 GLU cc_start: 0.7825 (tt0) cc_final: 0.7256 (tm-30) REVERT: A 454 LEU cc_start: 0.9152 (tp) cc_final: 0.8762 (tt) REVERT: B 27 ASP cc_start: 0.7097 (m-30) cc_final: 0.6783 (m-30) REVERT: B 287 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8674 (tp) REVERT: B 486 MET cc_start: 0.7420 (mtm) cc_final: 0.7034 (tpt) REVERT: B 500 ARG cc_start: 0.7127 (ttt180) cc_final: 0.6895 (ttt180) REVERT: C 5 ARG cc_start: 0.7323 (mtt90) cc_final: 0.7089 (mtm110) REVERT: C 56 ARG cc_start: 0.8102 (mtm-85) cc_final: 0.7856 (ptt90) REVERT: C 62 ASP cc_start: 0.7753 (m-30) cc_final: 0.7517 (m-30) REVERT: C 208 THR cc_start: 0.8448 (p) cc_final: 0.8066 (p) REVERT: C 259 MET cc_start: 0.7636 (mmm) cc_final: 0.7397 (mmm) REVERT: C 273 GLU cc_start: 0.5500 (OUTLIER) cc_final: 0.5214 (mp0) REVERT: C 278 TYR cc_start: 0.5580 (p90) cc_final: 0.4919 (p90) REVERT: D 202 LEU cc_start: 0.6114 (OUTLIER) cc_final: 0.5811 (mt) REVERT: D 241 ILE cc_start: 0.7371 (mp) cc_final: 0.7032 (mp) REVERT: D 249 ARG cc_start: 0.6327 (ttt90) cc_final: 0.6082 (ptm-80) REVERT: D 362 ASN cc_start: 0.8303 (p0) cc_final: 0.7875 (p0) REVERT: D 363 ASP cc_start: 0.6328 (t0) cc_final: 0.5792 (t0) outliers start: 34 outliers final: 25 residues processed: 200 average time/residue: 0.2497 time to fit residues: 75.4346 Evaluate side-chains 190 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 162 time to evaluate : 1.532 ------------------------------------------------------------------------------- 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 B residue 237 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 1 MET 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 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 174 VAL Chi-restraints excluded: chain D residue 202 LEU 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 24 optimal weight: 1.9990 chunk 152 optimal weight: 0.9980 chunk 85 optimal weight: 9.9990 chunk 193 optimal weight: 0.8980 chunk 178 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 190 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 111 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 335 GLN 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 = 0.136383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108107 restraints weight = 25388.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.106995 restraints weight = 35633.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.108407 restraints weight = 36201.874| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2018 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 : 0.555 7.314 20961 Z= 0.275 Chirality : 0.041 0.147 2416 Planarity : 0.004 0.045 2682 Dihedral : 4.234 20.247 2063 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 2.23 % Allowed : 16.16 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.20), residues: 1910 helix: 1.06 (0.19), residues: 813 sheet: -1.33 (0.32), residues: 256 loop : -2.57 (0.20), residues: 841 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 283 HIS 0.008 0.001 HIS C 157 PHE 0.012 0.001 PHE B 509 TYR 0.028 0.001 TYR C 107 ARG 0.005 0.000 ARG A 177 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 438) hydrogen bonds : angle 3.45958 ( 1314) metal coordination : bond 0.00314 ( 3) covalent geometry : bond 0.00317 (15411) covalent geometry : angle 0.55478 (20961) *********************** 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 205 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 168 time to evaluate : 1.617 Fit side-chains REVERT: A 373 GLU cc_start: 0.7932 (tt0) cc_final: 0.7284 (tm-30) REVERT: A 454 LEU cc_start: 0.9193 (tp) cc_final: 0.8841 (tt) REVERT: B 27 ASP cc_start: 0.7231 (m-30) cc_final: 0.6936 (m-30) REVERT: B 287 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8673 (tp) REVERT: B 486 MET cc_start: 0.7612 (mtm) cc_final: 0.7035 (tpt) REVERT: B 500 ARG cc_start: 0.7211 (ttt180) cc_final: 0.6994 (ttt180) REVERT: C 62 ASP cc_start: 0.7877 (m-30) cc_final: 0.7594 (m-30) REVERT: C 208 THR cc_start: 0.8477 (p) cc_final: 0.8077 (p) REVERT: C 259 MET cc_start: 0.7724 (mmm) cc_final: 0.7452 (mmm) REVERT: C 273 GLU cc_start: 0.5552 (OUTLIER) cc_final: 0.5266 (mp0) REVERT: C 278 TYR cc_start: 0.5585 (p90) cc_final: 0.4816 (p90) REVERT: D 241 ILE cc_start: 0.7435 (mp) cc_final: 0.7134 (mp) REVERT: D 249 ARG cc_start: 0.6435 (ttt90) cc_final: 0.5847 (ptm-80) REVERT: D 362 ASN cc_start: 0.8348 (p0) cc_final: 0.7943 (p0) REVERT: D 363 ASP cc_start: 0.6351 (t0) cc_final: 0.5792 (t0) outliers start: 37 outliers final: 30 residues processed: 195 average time/residue: 0.2564 time to fit residues: 75.7032 Evaluate side-chains 188 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 156 time to evaluate : 1.776 ------------------------------------------------------------------------------- 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 287 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL Chi-restraints excluded: chain C residue 1 MET 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 176 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 176 optimal weight: 10.0000 chunk 87 optimal weight: 0.7980 chunk 161 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 160 optimal weight: 0.7980 chunk 186 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 34 optimal weight: 0.9990 chunk 114 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 284 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.137003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.108302 restraints weight = 25303.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.108328 restraints weight = 34640.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.110052 restraints weight = 28224.798| |-----------------------------------------------------------------------------| r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2173 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= 0.115 Angle : 0.546 7.609 20961 Z= 0.270 Chirality : 0.041 0.146 2416 Planarity : 0.005 0.084 2682 Dihedral : 4.158 20.131 2063 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 2.29 % Allowed : 16.77 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.20), residues: 1910 helix: 1.18 (0.19), residues: 813 sheet: -1.42 (0.32), residues: 255 loop : -2.44 (0.21), residues: 842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.011 0.001 PHE B 509 TYR 0.028 0.001 TYR C 107 ARG 0.006 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 438) hydrogen bonds : angle 3.38587 ( 1314) metal coordination : bond 0.00230 ( 3) covalent geometry : bond 0.00273 (15411) covalent geometry : angle 0.54647 (20961) *********************** 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 200 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.556 Fit side-chains REVERT: A 373 GLU cc_start: 0.7901 (tt0) cc_final: 0.7276 (tm-30) REVERT: A 454 LEU cc_start: 0.9182 (tp) cc_final: 0.8784 (tt) REVERT: B 27 ASP cc_start: 0.7240 (m-30) cc_final: 0.6944 (m-30) REVERT: B 184 MET cc_start: 0.7896 (tpt) cc_final: 0.7645 (mmm) REVERT: B 287 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8687 (tp) REVERT: B 486 MET cc_start: 0.7594 (mtm) cc_final: 0.7063 (tpt) REVERT: B 489 MET cc_start: 0.6422 (ttm) cc_final: 0.6087 (ttm) REVERT: B 500 ARG cc_start: 0.7216 (ttt180) cc_final: 0.6978 (ttt-90) REVERT: C 62 ASP cc_start: 0.7698 (m-30) cc_final: 0.7430 (m-30) REVERT: C 208 THR cc_start: 0.8436 (p) cc_final: 0.8034 (p) REVERT: C 259 MET cc_start: 0.7953 (mmm) cc_final: 0.7725 (mmm) REVERT: C 273 GLU cc_start: 0.5266 (OUTLIER) cc_final: 0.4993 (mp0) REVERT: C 278 TYR cc_start: 0.5560 (p90) cc_final: 0.4860 (p90) REVERT: C 310 ARG cc_start: 0.6729 (ttp80) cc_final: 0.6469 (ttp80) REVERT: D 207 GLN cc_start: 0.6321 (tm-30) cc_final: 0.5996 (tm-30) REVERT: D 241 ILE cc_start: 0.7330 (mp) cc_final: 0.7021 (mp) REVERT: D 249 ARG cc_start: 0.6386 (ttt90) cc_final: 0.5828 (ptm-80) REVERT: D 362 ASN cc_start: 0.8318 (p0) cc_final: 0.7911 (p0) REVERT: D 363 ASP cc_start: 0.6340 (t0) cc_final: 0.5774 (t0) outliers start: 38 outliers final: 32 residues processed: 191 average time/residue: 0.2410 time to fit residues: 69.9469 Evaluate side-chains 189 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 155 time to evaluate : 1.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR 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 12 LEU Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 194 random chunks: chunk 117 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 95 optimal weight: 0.0040 chunk 39 optimal weight: 0.8980 chunk 143 optimal weight: 0.9980 chunk 74 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 13 optimal weight: 0.0980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.138363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.110946 restraints weight = 25047.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.109213 restraints weight = 40108.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.110836 restraints weight = 37151.336| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15414 Z= 0.098 Angle : 0.535 8.085 20961 Z= 0.264 Chirality : 0.040 0.142 2416 Planarity : 0.004 0.044 2682 Dihedral : 3.993 19.799 2063 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.81 % Allowed : 17.25 % Favored : 80.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.20), residues: 1910 helix: 1.33 (0.19), residues: 812 sheet: -1.49 (0.31), residues: 282 loop : -2.28 (0.21), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.010 0.001 PHE B 509 TYR 0.025 0.001 TYR C 107 ARG 0.016 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.02761 ( 438) hydrogen bonds : angle 3.32985 ( 1314) metal coordination : bond 0.00221 ( 3) covalent geometry : bond 0.00226 (15411) covalent geometry : angle 0.53459 (20961) *********************** 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 194 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 1.681 Fit side-chains REVERT: A 373 GLU cc_start: 0.7871 (tt0) cc_final: 0.7275 (tm-30) REVERT: A 454 LEU cc_start: 0.9078 (tp) cc_final: 0.8653 (tt) REVERT: B 27 ASP cc_start: 0.7206 (m-30) cc_final: 0.6919 (m-30) REVERT: B 93 LEU cc_start: 0.6118 (OUTLIER) cc_final: 0.5799 (tt) REVERT: B 184 MET cc_start: 0.7946 (tpt) cc_final: 0.7671 (mmm) REVERT: B 287 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8698 (tp) REVERT: B 486 MET cc_start: 0.7577 (mtm) cc_final: 0.6762 (tpt) REVERT: B 489 MET cc_start: 0.6321 (ttm) cc_final: 0.5996 (ttm) REVERT: B 500 ARG cc_start: 0.7169 (ttt180) cc_final: 0.6926 (ttt-90) REVERT: C 56 ARG cc_start: 0.8045 (mtm-85) cc_final: 0.7776 (ptt90) REVERT: C 62 ASP cc_start: 0.7631 (m-30) cc_final: 0.7368 (m-30) REVERT: C 208 THR cc_start: 0.8489 (p) cc_final: 0.8113 (p) REVERT: C 273 GLU cc_start: 0.5182 (OUTLIER) cc_final: 0.4929 (mp0) REVERT: C 278 TYR cc_start: 0.5574 (p90) cc_final: 0.4843 (p90) REVERT: C 310 ARG cc_start: 0.6718 (ttp80) cc_final: 0.6496 (ttp80) REVERT: C 327 MET cc_start: 0.7227 (ptp) cc_final: 0.6851 (ptp) REVERT: C 387 MET cc_start: 0.7104 (mtt) cc_final: 0.6822 (mtt) REVERT: D 241 ILE cc_start: 0.7313 (mp) cc_final: 0.6978 (mp) REVERT: D 249 ARG cc_start: 0.6453 (ttt90) cc_final: 0.6092 (ptm-80) REVERT: D 362 ASN cc_start: 0.8291 (p0) cc_final: 0.7877 (p0) REVERT: D 363 ASP cc_start: 0.6212 (t0) cc_final: 0.5656 (t0) outliers start: 30 outliers final: 26 residues processed: 188 average time/residue: 0.2542 time to fit residues: 72.4604 Evaluate side-chains 184 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 2.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR 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 12 LEU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 287 LEU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain B residue 504 VAL 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 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 158 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 35 optimal weight: 0.0050 chunk 113 optimal weight: 0.0010 chunk 65 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 115 optimal weight: 3.9990 overall best weight: 0.4800 ------------------------------------------------------------------------------- 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** C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.138945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110404 restraints weight = 25041.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.109264 restraints weight = 35378.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.110256 restraints weight = 36261.454| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.2518 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= 0.095 Angle : 0.536 8.356 20961 Z= 0.263 Chirality : 0.040 0.155 2416 Planarity : 0.004 0.043 2682 Dihedral : 3.865 19.489 2063 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.99 % Allowed : 17.31 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.20), residues: 1910 helix: 1.50 (0.19), residues: 807 sheet: -1.34 (0.32), residues: 280 loop : -2.15 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.010 0.001 PHE B 509 TYR 0.026 0.001 TYR C 107 ARG 0.015 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.02670 ( 438) hydrogen bonds : angle 3.27438 ( 1314) metal coordination : bond 0.00266 ( 3) covalent geometry : bond 0.00218 (15411) covalent geometry : angle 0.53598 (20961) *********************** 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 : 1.616 Fit side-chains revert: symmetry clash REVERT: A 373 GLU cc_start: 0.7843 (tt0) cc_final: 0.7259 (tm-30) REVERT: A 591 SER cc_start: 0.8331 (t) cc_final: 0.7908 (p) REVERT: B 1 MET cc_start: 0.5832 (tmm) cc_final: 0.5627 (tmm) REVERT: B 27 ASP cc_start: 0.7215 (m-30) cc_final: 0.6918 (m-30) REVERT: B 93 LEU cc_start: 0.6141 (OUTLIER) cc_final: 0.5783 (tt) REVERT: B 486 MET cc_start: 0.7595 (mtm) cc_final: 0.6856 (tpt) REVERT: B 489 MET cc_start: 0.6328 (ttm) cc_final: 0.5989 (ttm) REVERT: B 500 ARG cc_start: 0.7140 (ttt180) cc_final: 0.6873 (ttt-90) REVERT: C 62 ASP cc_start: 0.7682 (m-30) cc_final: 0.7472 (m-30) REVERT: C 208 THR cc_start: 0.8662 (p) cc_final: 0.8341 (p) REVERT: C 273 GLU cc_start: 0.5241 (OUTLIER) cc_final: 0.4991 (mp0) REVERT: C 278 TYR cc_start: 0.5530 (p90) cc_final: 0.4873 (p90) REVERT: C 437 MET cc_start: 0.7434 (ttt) cc_final: 0.7210 (ttt) REVERT: D 241 ILE cc_start: 0.7310 (mp) cc_final: 0.6974 (mp) REVERT: D 249 ARG cc_start: 0.6424 (ttt90) cc_final: 0.6051 (ptm-80) REVERT: D 362 ASN cc_start: 0.8293 (p0) cc_final: 0.7874 (p0) REVERT: D 363 ASP cc_start: 0.6121 (t0) cc_final: 0.5531 (t0) outliers start: 33 outliers final: 29 residues processed: 194 average time/residue: 0.2676 time to fit residues: 78.9294 Evaluate side-chains 190 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR 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 12 LEU Chi-restraints excluded: chain B residue 88 THR 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 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 45 optimal weight: 3.9990 chunk 146 optimal weight: 0.0170 chunk 183 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 37 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 123 optimal weight: 0.0370 chunk 84 optimal weight: 6.9990 chunk 141 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 167 optimal weight: 9.9990 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 219 ASN ** B 246 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 276 ASN C 346 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.139216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.111725 restraints weight = 25164.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.110725 restraints weight = 36951.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.112087 restraints weight = 31451.071| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15414 Z= 0.097 Angle : 0.544 10.334 20961 Z= 0.265 Chirality : 0.041 0.158 2416 Planarity : 0.004 0.045 2682 Dihedral : 3.829 18.751 2063 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 2.17 % Allowed : 17.37 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.20), residues: 1910 helix: 1.56 (0.19), residues: 807 sheet: -1.22 (0.32), residues: 284 loop : -2.10 (0.21), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.018 0.001 PHE A 705 TYR 0.026 0.001 TYR C 107 ARG 0.015 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.02713 ( 438) hydrogen bonds : angle 3.26115 ( 1314) metal coordination : bond 0.00254 ( 3) covalent geometry : bond 0.00224 (15411) covalent geometry : angle 0.54378 (20961) ********************** 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 201 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 165 time to evaluate : 1.590 Fit side-chains REVERT: A 373 GLU cc_start: 0.7813 (tt0) cc_final: 0.7282 (tm-30) REVERT: A 591 SER cc_start: 0.8309 (t) cc_final: 0.7876 (p) REVERT: B 27 ASP cc_start: 0.7199 (m-30) cc_final: 0.6889 (m-30) REVERT: B 93 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5815 (tt) REVERT: B 500 ARG cc_start: 0.7098 (ttt180) cc_final: 0.6861 (ttt180) REVERT: C 62 ASP cc_start: 0.7579 (m-30) cc_final: 0.7347 (m-30) REVERT: C 208 THR cc_start: 0.8568 (p) cc_final: 0.8252 (p) REVERT: C 273 GLU cc_start: 0.5179 (OUTLIER) cc_final: 0.4826 (mp0) REVERT: C 278 TYR cc_start: 0.5570 (p90) cc_final: 0.4907 (p90) REVERT: D 241 ILE cc_start: 0.7054 (OUTLIER) cc_final: 0.6663 (mp) REVERT: D 249 ARG cc_start: 0.6413 (ttt90) cc_final: 0.6064 (ptm-80) REVERT: D 362 ASN cc_start: 0.8274 (p0) cc_final: 0.7861 (p0) REVERT: D 363 ASP cc_start: 0.6224 (t0) cc_final: 0.5671 (t0) outliers start: 36 outliers final: 31 residues processed: 193 average time/residue: 0.2390 time to fit residues: 70.7444 Evaluate side-chains 196 residues out of total 1688 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 162 time to evaluate : 1.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 THR 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 701 PHE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 88 THR 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 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 241 ILE 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 118 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 116 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 92 optimal weight: 10.0000 chunk 59 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 131 optimal weight: 0.5980 chunk 91 optimal weight: 4.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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** C 119 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.137360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109810 restraints weight = 25121.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.110227 restraints weight = 39132.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.111113 restraints weight = 36228.777| |-----------------------------------------------------------------------------| r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15414 Z= 0.137 Angle : 0.577 10.752 20961 Z= 0.282 Chirality : 0.042 0.194 2416 Planarity : 0.004 0.055 2682 Dihedral : 3.986 19.549 2063 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.39 % Favored : 93.61 % Rotamer: Outliers : 2.23 % Allowed : 17.61 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.20), residues: 1910 helix: 1.48 (0.19), residues: 808 sheet: -1.14 (0.31), residues: 292 loop : -2.18 (0.21), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.001 TRP D 283 HIS 0.007 0.001 HIS C 157 PHE 0.011 0.001 PHE B 509 TYR 0.027 0.001 TYR C 107 ARG 0.012 0.000 ARG A 785 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 438) hydrogen bonds : angle 3.37810 ( 1314) metal coordination : bond 0.00318 ( 3) covalent geometry : bond 0.00329 (15411) covalent geometry : angle 0.57735 (20961) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3971.76 seconds wall clock time: 70 minutes 52.62 seconds (4252.62 seconds total)