Starting phenix.real_space_refine on Wed Sep 17 07:08:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xt9_38641/09_2025/8xt9_38641.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xt9_38641/09_2025/8xt9_38641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8xt9_38641/09_2025/8xt9_38641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xt9_38641/09_2025/8xt9_38641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xt9_38641/09_2025/8xt9_38641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xt9_38641/09_2025/8xt9_38641.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 4186 2.51 5 N 1075 2.21 5 O 1184 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6479 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 5740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 737, 5740 Classifications: {'peptide': 737} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 37, 'TRANS': 699} Chain breaks: 3 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "A" Number of atoms: 739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 739 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 3, 'TYR:plan': 3, 'PHE:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 49 Time building chain proxies: 1.41, per 1000 atoms: 0.22 Number of scatterers: 6479 At special positions: 0 Unit cell: (69.615, 89.964, 171.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 1184 8.00 N 1075 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 29 " - pdb=" SG CYS C 35 " distance=2.02 Simple disulfide: pdb=" SG CYS C 33 " - pdb=" SG CYS C 43 " distance=2.03 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 364 " distance=2.03 Simple disulfide: pdb=" SG CYS C 618 " - pdb=" SG CYS C 693 " distance=2.03 Simple disulfide: pdb=" SG CYS C 757 " - pdb=" SG CYS C 761 " distance=2.57 Simple disulfide: pdb=" SG CYS A 428 " - pdb=" SG CYS A 501 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 339.3 milliseconds Enol-peptide restraints added in 1.2 microseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1586 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 8 sheets defined 34.1% alpha, 12.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'C' and resid 121 through 127 removed outlier: 3.588A pdb=" N ILE C 125 " --> pdb=" O PRO C 121 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ARG C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 176 removed outlier: 4.272A pdb=" N LEU C 176 " --> pdb=" O PRO C 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 247 Processing helix chain 'C' and resid 289 through 292 removed outlier: 4.131A pdb=" N PHE C 292 " --> pdb=" O ASN C 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 289 through 292' Processing helix chain 'C' and resid 337 through 342 Processing helix chain 'C' and resid 466 through 471 removed outlier: 3.928A pdb=" N CYS C 470 " --> pdb=" O TYR C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 566 Processing helix chain 'C' and resid 571 through 601 removed outlier: 3.849A pdb=" N PHE C 586 " --> pdb=" O VAL C 582 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N MET C 587 " --> pdb=" O SER C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 614 removed outlier: 3.656A pdb=" N PHE C 608 " --> pdb=" O ARG C 604 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ILE C 610 " --> pdb=" O ALA C 606 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N TRP C 611 " --> pdb=" O GLU C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 649 removed outlier: 3.942A pdb=" N LYS C 619 " --> pdb=" O GLY C 615 " (cutoff:3.500A) Processing helix chain 'C' and resid 657 through 679 removed outlier: 3.922A pdb=" N GLN C 661 " --> pdb=" O ASN C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 680 through 682 No H-bonds generated for 'chain 'C' and resid 680 through 682' Processing helix chain 'C' and resid 703 through 732 removed outlier: 4.055A pdb=" N THR C 707 " --> pdb=" O SER C 703 " (cutoff:3.500A) Processing helix chain 'C' and resid 745 through 769 Proline residue: C 762 - end of helix Processing helix chain 'C' and resid 770 through 772 No H-bonds generated for 'chain 'C' and resid 770 through 772' Processing helix chain 'C' and resid 778 through 790 Processing helix chain 'C' and resid 791 through 804 Proline residue: C 798 - end of helix Processing helix chain 'C' and resid 805 through 821 Processing helix chain 'A' and resid 459 through 461 No H-bonds generated for 'chain 'A' and resid 459 through 461' Processing helix chain 'A' and resid 467 through 470 removed outlier: 4.124A pdb=" N LYS A 470 " --> pdb=" O ASP A 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 467 through 470' Processing helix chain 'A' and resid 492 through 496 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.790A pdb=" N ILE A 517 " --> pdb=" O ASN A 514 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 35 through 36 removed outlier: 3.773A pdb=" N ARG C 40 " --> pdb=" O ASP C 36 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 158 " --> pdb=" O THR C 183 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP C 231 " --> pdb=" O LEU C 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'C' and resid 191 through 192 removed outlier: 4.115A pdb=" N ILE C 192 " --> pdb=" O SER C 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 262 through 263 Processing sheet with id=AA5, first strand: chain 'C' and resid 300 through 304 removed outlier: 6.527A pdb=" N LEU C 301 " --> pdb=" O THR C 325 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N THR C 327 " --> pdb=" O LEU C 301 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N ILE C 303 " --> pdb=" O THR C 327 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU C 348 " --> pdb=" O SER C 371 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LEU C 418 " --> pdb=" O LYS C 440 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 425 through 429 Processing sheet with id=AA7, first strand: chain 'A' and resid 463 through 465 removed outlier: 5.318A pdb=" N GLY A 453 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG A 444 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 455 " --> pdb=" O TRP A 442 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 463 through 465 removed outlier: 5.318A pdb=" N GLY A 453 " --> pdb=" O ARG A 444 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ARG A 444 " --> pdb=" O GLY A 453 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ALA A 455 " --> pdb=" O TRP A 442 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 1039 1.26 - 1.40: 1636 1.40 - 1.55: 3898 1.55 - 1.69: 12 1.69 - 1.83: 45 Bond restraints: 6630 Sorted by residual: bond pdb=" N PRO C 193 " pdb=" CD PRO C 193 " ideal model delta sigma weight residual 1.473 1.293 0.180 1.40e-02 5.10e+03 1.65e+02 bond pdb=" C GLN C 180 " pdb=" O GLN C 180 " ideal model delta sigma weight residual 1.235 1.120 0.115 1.24e-02 6.50e+03 8.64e+01 bond pdb=" CA ASP C 147 " pdb=" C ASP C 147 " ideal model delta sigma weight residual 1.525 1.647 -0.122 1.38e-02 5.25e+03 7.82e+01 bond pdb=" C CYS C 757 " pdb=" O CYS C 757 " ideal model delta sigma weight residual 1.237 1.137 0.100 1.16e-02 7.43e+03 7.42e+01 bond pdb=" C MET C 782 " pdb=" O MET C 782 " ideal model delta sigma weight residual 1.236 1.141 0.095 1.15e-02 7.56e+03 6.88e+01 ... (remaining 6625 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.91: 8799 3.91 - 7.82: 188 7.82 - 11.74: 25 11.74 - 15.65: 6 15.65 - 19.56: 3 Bond angle restraints: 9021 Sorted by residual: angle pdb=" N SER C 148 " pdb=" CA SER C 148 " pdb=" C SER C 148 " ideal model delta sigma weight residual 110.55 90.99 19.56 1.35e+00 5.49e-01 2.10e+02 angle pdb=" N GLU C 146 " pdb=" CA GLU C 146 " pdb=" C GLU C 146 " ideal model delta sigma weight residual 111.11 125.81 -14.70 1.20e+00 6.94e-01 1.50e+02 angle pdb=" N ASN A 489 " pdb=" CA ASN A 489 " pdb=" C ASN A 489 " ideal model delta sigma weight residual 109.50 127.94 -18.44 1.58e+00 4.01e-01 1.36e+02 angle pdb=" C ASP C 147 " pdb=" CA ASP C 147 " pdb=" CB ASP C 147 " ideal model delta sigma weight residual 111.06 94.50 16.56 1.55e+00 4.16e-01 1.14e+02 angle pdb=" N VAL C 204 " pdb=" CA VAL C 204 " pdb=" C VAL C 204 " ideal model delta sigma weight residual 111.81 119.89 -8.08 8.60e-01 1.35e+00 8.83e+01 ... (remaining 9016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 3355 17.17 - 34.33: 421 34.33 - 51.50: 127 51.50 - 68.66: 34 68.66 - 85.83: 4 Dihedral angle restraints: 3941 sinusoidal: 1501 harmonic: 2440 Sorted by residual: dihedral pdb=" CD ARG C 275 " pdb=" NE ARG C 275 " pdb=" CZ ARG C 275 " pdb=" NH1 ARG C 275 " ideal model delta sinusoidal sigma weight residual 0.00 67.65 -67.65 1 1.00e+01 1.00e-02 5.95e+01 dihedral pdb=" C ASP C 147 " pdb=" N ASP C 147 " pdb=" CA ASP C 147 " pdb=" CB ASP C 147 " ideal model delta harmonic sigma weight residual -122.60 -104.56 -18.04 0 2.50e+00 1.60e-01 5.21e+01 dihedral pdb=" C ASP C 162 " pdb=" N ASP C 162 " pdb=" CA ASP C 162 " pdb=" CB ASP C 162 " ideal model delta harmonic sigma weight residual -122.60 -140.53 17.93 0 2.50e+00 1.60e-01 5.14e+01 ... (remaining 3938 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.135: 974 0.135 - 0.269: 71 0.269 - 0.404: 7 0.404 - 0.538: 3 0.538 - 0.672: 2 Chirality restraints: 1057 Sorted by residual: chirality pdb=" CA ASP C 162 " pdb=" N ASP C 162 " pdb=" C ASP C 162 " pdb=" CB ASP C 162 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.13e+01 chirality pdb=" CA GLU C 146 " pdb=" N GLU C 146 " pdb=" C GLU C 146 " pdb=" CB GLU C 146 " both_signs ideal model delta sigma weight residual False 2.51 1.86 0.65 2.00e-01 2.50e+01 1.06e+01 chirality pdb=" CA ASP C 147 " pdb=" N ASP C 147 " pdb=" C ASP C 147 " pdb=" CB ASP C 147 " both_signs ideal model delta sigma weight residual False 2.51 3.03 -0.52 2.00e-01 2.50e+01 6.72e+00 ... (remaining 1054 not shown) Planarity restraints: 1142 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 275 " 1.003 9.50e-02 1.11e+02 4.50e-01 1.22e+02 pdb=" NE ARG C 275 " -0.062 2.00e-02 2.50e+03 pdb=" CZ ARG C 275 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG C 275 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG C 275 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 493 " -0.027 2.00e-02 2.50e+03 4.97e-02 2.47e+01 pdb=" C PRO A 493 " 0.086 2.00e-02 2.50e+03 pdb=" O PRO A 493 " -0.030 2.00e-02 2.50e+03 pdb=" N GLU A 494 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET C 782 " -0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C MET C 782 " 0.085 2.00e-02 2.50e+03 pdb=" O MET C 782 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS C 783 " -0.029 2.00e-02 2.50e+03 ... (remaining 1139 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1655 2.79 - 3.32: 6090 3.32 - 3.85: 10590 3.85 - 4.37: 12239 4.37 - 4.90: 21019 Nonbonded interactions: 51593 Sorted by model distance: nonbonded pdb=" N SER C 148 " pdb=" O SER C 148 " model vdw 2.268 2.496 nonbonded pdb=" O HIS C 365 " pdb=" OG SER C 390 " model vdw 2.327 3.040 nonbonded pdb=" OE1 GLU C 686 " pdb=" OG SER C 703 " model vdw 2.351 3.040 nonbonded pdb=" O THR C 526 " pdb=" OG1 THR C 526 " model vdw 2.382 3.040 nonbonded pdb=" O PRO A 447 " pdb=" NZ LYS A 449 " model vdw 2.386 3.120 ... (remaining 51588 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 2.280 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.030 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 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 : 0.010 0.541 6636 Z= 0.574 Angle : 1.319 19.559 9033 Z= 0.864 Chirality : 0.084 0.672 1057 Planarity : 0.015 0.450 1142 Dihedral : 17.170 85.831 2337 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.01 % Favored : 93.39 % Rotamer: Outliers : 6.04 % Allowed : 26.83 % Favored : 67.13 % Cbeta Deviations : 0.63 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.55 (0.29), residues: 832 helix: 1.19 (0.33), residues: 247 sheet: -0.72 (0.48), residues: 133 loop : -1.14 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 275 TYR 0.013 0.001 TYR C 725 PHE 0.022 0.001 PHE C 554 TRP 0.008 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00693 ( 6630) covalent geometry : angle 1.30344 ( 9021) SS BOND : bond 0.22106 ( 6) SS BOND : angle 5.68589 ( 12) hydrogen bonds : bond 0.16162 ( 244) hydrogen bonds : angle 6.15306 ( 735) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 80 time to evaluate : 0.199 Fit side-chains REVERT: C 440 LYS cc_start: 0.8571 (mtpp) cc_final: 0.8304 (mttp) REVERT: C 659 LEU cc_start: 0.7133 (OUTLIER) cc_final: 0.6850 (pt) REVERT: A 445 GLN cc_start: 0.6414 (tp40) cc_final: 0.5246 (tp40) REVERT: A 485 TYR cc_start: 0.8931 (m-80) cc_final: 0.8503 (m-80) outliers start: 43 outliers final: 18 residues processed: 113 average time/residue: 0.0747 time to fit residues: 11.3806 Evaluate side-chains 78 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 59 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 261 SER Chi-restraints excluded: chain C residue 262 VAL Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 373 GLN Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 464 VAL Chi-restraints excluded: chain C residue 532 CYS Chi-restraints excluded: chain C residue 538 SER Chi-restraints excluded: chain C residue 541 ILE Chi-restraints excluded: chain C residue 557 LEU Chi-restraints excluded: chain C residue 575 LEU Chi-restraints excluded: chain C residue 579 LEU Chi-restraints excluded: chain C residue 641 VAL Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 704 LEU Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 0.0170 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 62 optimal weight: 0.0070 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.0980 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 7.9990 overall best weight: 0.3036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 187 ASN C 402 HIS C 444 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.118310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.088599 restraints weight = 13275.199| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 3.30 r_work: 0.3279 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.1312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6636 Z= 0.115 Angle : 0.608 7.579 9033 Z= 0.300 Chirality : 0.044 0.182 1057 Planarity : 0.004 0.036 1142 Dihedral : 6.397 54.159 910 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.49 % Allowed : 27.81 % Favored : 67.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.29), residues: 832 helix: 1.72 (0.32), residues: 256 sheet: -0.52 (0.48), residues: 135 loop : -0.86 (0.28), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 817 TYR 0.008 0.001 TYR C 725 PHE 0.013 0.001 PHE C 760 TRP 0.005 0.001 TRP C 546 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 6630) covalent geometry : angle 0.60595 ( 9021) SS BOND : bond 0.01099 ( 6) SS BOND : angle 1.39021 ( 12) hydrogen bonds : bond 0.04089 ( 244) hydrogen bonds : angle 4.49254 ( 735) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 65 time to evaluate : 0.181 Fit side-chains REVERT: C 71 GLN cc_start: 0.8663 (pp30) cc_final: 0.8216 (pp30) REVERT: C 519 ILE cc_start: 0.7596 (OUTLIER) cc_final: 0.7173 (tp) REVERT: C 532 CYS cc_start: 0.8672 (m) cc_final: 0.8467 (t) REVERT: C 659 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6503 (pp) REVERT: C 667 LEU cc_start: 0.9140 (OUTLIER) cc_final: 0.8776 (tm) REVERT: A 440 MET cc_start: 0.6787 (tmm) cc_final: 0.6506 (tmm) REVERT: A 445 GLN cc_start: 0.7214 (tp40) cc_final: 0.6734 (tp40) REVERT: A 459 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7809 (mm) REVERT: A 485 TYR cc_start: 0.8745 (m-80) cc_final: 0.8521 (m-80) outliers start: 32 outliers final: 15 residues processed: 92 average time/residue: 0.0542 time to fit residues: 7.3442 Evaluate side-chains 79 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 293 HIS Chi-restraints excluded: chain C residue 412 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 21 optimal weight: 0.8980 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 0.1980 chunk 66 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 65 optimal weight: 10.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.115567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.085936 restraints weight = 13336.446| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 3.29 r_work: 0.3211 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6636 Z= 0.137 Angle : 0.600 7.356 9033 Z= 0.295 Chirality : 0.044 0.167 1057 Planarity : 0.004 0.036 1142 Dihedral : 5.149 55.246 887 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 4.21 % Allowed : 29.07 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.29), residues: 832 helix: 1.96 (0.32), residues: 255 sheet: -0.57 (0.48), residues: 135 loop : -0.86 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 542 TYR 0.009 0.001 TYR C 725 PHE 0.011 0.001 PHE C 808 TRP 0.008 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6630) covalent geometry : angle 0.59865 ( 9021) SS BOND : bond 0.00752 ( 6) SS BOND : angle 1.31228 ( 12) hydrogen bonds : bond 0.03955 ( 244) hydrogen bonds : angle 4.31044 ( 735) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.160 Fit side-chains REVERT: C 165 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.7987 (pp) REVERT: C 260 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8522 (tp) REVERT: C 519 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7194 (tp) REVERT: C 659 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6585 (pp) REVERT: C 667 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8540 (tm) REVERT: C 671 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8458 (mm) REVERT: C 721 MET cc_start: 0.8822 (ptp) cc_final: 0.8575 (ptp) REVERT: C 725 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.7337 (m-80) REVERT: A 445 GLN cc_start: 0.7335 (tp40) cc_final: 0.6816 (tp40) REVERT: A 485 TYR cc_start: 0.8699 (m-80) cc_final: 0.8488 (m-80) outliers start: 30 outliers final: 16 residues processed: 82 average time/residue: 0.0487 time to fit residues: 6.0552 Evaluate side-chains 78 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 51 VAL Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 93 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 12 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 50 optimal weight: 0.2980 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.111905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.082533 restraints weight = 13307.408| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 3.23 r_work: 0.3146 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 6636 Z= 0.228 Angle : 0.647 7.318 9033 Z= 0.322 Chirality : 0.046 0.190 1057 Planarity : 0.004 0.042 1142 Dihedral : 5.191 55.197 885 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 5.20 % Allowed : 28.23 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.29), residues: 832 helix: 2.15 (0.32), residues: 249 sheet: -0.57 (0.47), residues: 132 loop : -0.88 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 542 TYR 0.011 0.001 TYR C 466 PHE 0.012 0.001 PHE C 473 TRP 0.017 0.001 TRP C 159 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 6630) covalent geometry : angle 0.64548 ( 9021) SS BOND : bond 0.00815 ( 6) SS BOND : angle 1.44231 ( 12) hydrogen bonds : bond 0.04581 ( 244) hydrogen bonds : angle 4.39203 ( 735) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 57 time to evaluate : 0.223 Fit side-chains revert: symmetry clash REVERT: C 165 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8018 (pp) REVERT: C 247 LEU cc_start: 0.9121 (OUTLIER) cc_final: 0.8916 (pp) REVERT: C 367 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8785 (tp) REVERT: C 519 ILE cc_start: 0.7642 (OUTLIER) cc_final: 0.7210 (tp) REVERT: C 659 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.6978 (pp) REVERT: C 667 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8663 (tm) REVERT: C 671 LEU cc_start: 0.8703 (OUTLIER) cc_final: 0.8460 (mm) REVERT: C 725 TYR cc_start: 0.8900 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: A 445 GLN cc_start: 0.7488 (tp40) cc_final: 0.7153 (tp40) REVERT: A 485 TYR cc_start: 0.8789 (m-80) cc_final: 0.8556 (m-80) REVERT: A 498 MET cc_start: 0.7475 (tpt) cc_final: 0.7154 (tpt) outliers start: 37 outliers final: 18 residues processed: 87 average time/residue: 0.0511 time to fit residues: 6.8494 Evaluate side-chains 83 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 247 LEU Chi-restraints excluded: chain C residue 260 ILE Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 671 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 501 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 48 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 62 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 139 ASN C 293 HIS C 658 HIS C 714 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.113979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.084871 restraints weight = 13185.287| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.23 r_work: 0.3221 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 6636 Z= 0.132 Angle : 0.590 8.312 9033 Z= 0.288 Chirality : 0.043 0.151 1057 Planarity : 0.004 0.046 1142 Dihedral : 4.926 54.286 885 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.48 % Allowed : 27.67 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.29), residues: 832 helix: 2.27 (0.32), residues: 250 sheet: -0.56 (0.48), residues: 128 loop : -0.85 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 542 TYR 0.010 0.001 TYR C 725 PHE 0.011 0.001 PHE C 760 TRP 0.008 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6630) covalent geometry : angle 0.58878 ( 9021) SS BOND : bond 0.00691 ( 6) SS BOND : angle 1.32230 ( 12) hydrogen bonds : bond 0.03912 ( 244) hydrogen bonds : angle 4.19065 ( 735) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 58 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: C 62 LEU cc_start: 0.7637 (OUTLIER) cc_final: 0.7231 (tt) REVERT: C 66 MET cc_start: 0.8784 (mpp) cc_final: 0.8528 (mpp) REVERT: C 83 LEU cc_start: 0.8847 (OUTLIER) cc_final: 0.8504 (tt) REVERT: C 165 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.7941 (pp) REVERT: C 344 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8485 (mtm) REVERT: C 367 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8736 (tp) REVERT: C 381 LYS cc_start: 0.9309 (mttt) cc_final: 0.8995 (mtpp) REVERT: C 519 ILE cc_start: 0.7590 (OUTLIER) cc_final: 0.7125 (tp) REVERT: C 659 LEU cc_start: 0.7511 (OUTLIER) cc_final: 0.6939 (pp) REVERT: C 667 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8590 (tm) REVERT: C 725 TYR cc_start: 0.8808 (OUTLIER) cc_final: 0.7258 (m-80) REVERT: A 445 GLN cc_start: 0.7321 (tp40) cc_final: 0.6962 (tp40) REVERT: A 463 THR cc_start: 0.8813 (p) cc_final: 0.8421 (m) REVERT: A 484 LEU cc_start: 0.7211 (tp) cc_final: 0.7008 (tp) REVERT: A 485 TYR cc_start: 0.8900 (m-80) cc_final: 0.8673 (m-80) outliers start: 39 outliers final: 20 residues processed: 88 average time/residue: 0.0542 time to fit residues: 7.1716 Evaluate side-chains 87 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 58 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 86 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 139 ASN Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 53 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 0.0570 chunk 32 optimal weight: 0.4980 chunk 76 optimal weight: 0.0870 chunk 24 optimal weight: 0.7980 chunk 11 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.3054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.116048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.086540 restraints weight = 13440.516| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 3.32 r_work: 0.3252 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 6636 Z= 0.104 Angle : 0.585 8.110 9033 Z= 0.280 Chirality : 0.043 0.149 1057 Planarity : 0.004 0.047 1142 Dihedral : 4.705 52.170 885 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 3.65 % Allowed : 29.21 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.27 (0.29), residues: 832 helix: 2.14 (0.32), residues: 256 sheet: -0.53 (0.48), residues: 128 loop : -0.77 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 506 TYR 0.009 0.001 TYR C 725 PHE 0.010 0.001 PHE C 760 TRP 0.008 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00242 ( 6630) covalent geometry : angle 0.58296 ( 9021) SS BOND : bond 0.00640 ( 6) SS BOND : angle 1.30417 ( 12) hydrogen bonds : bond 0.03490 ( 244) hydrogen bonds : angle 4.07072 ( 735) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 61 time to evaluate : 0.187 Fit side-chains REVERT: C 62 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7252 (tt) REVERT: C 66 MET cc_start: 0.8782 (mpp) cc_final: 0.8517 (mpp) REVERT: C 165 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.7929 (pp) REVERT: C 367 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8677 (tp) REVERT: C 381 LYS cc_start: 0.9268 (mttt) cc_final: 0.8962 (mtpp) REVERT: C 519 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.7121 (tp) REVERT: C 659 LEU cc_start: 0.7566 (OUTLIER) cc_final: 0.7010 (pp) REVERT: C 667 LEU cc_start: 0.8988 (OUTLIER) cc_final: 0.8670 (tm) REVERT: C 725 TYR cc_start: 0.8627 (OUTLIER) cc_final: 0.7404 (m-80) REVERT: A 445 GLN cc_start: 0.7248 (tp40) cc_final: 0.6873 (tp40) REVERT: A 463 THR cc_start: 0.8797 (p) cc_final: 0.8491 (m) outliers start: 26 outliers final: 17 residues processed: 82 average time/residue: 0.0508 time to fit residues: 6.3620 Evaluate side-chains 81 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 57 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 659 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 681 LEU Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 33 optimal weight: 0.0570 chunk 44 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 53 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.114344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.085255 restraints weight = 13028.425| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 3.23 r_work: 0.3231 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6636 Z= 0.132 Angle : 0.606 8.259 9033 Z= 0.293 Chirality : 0.044 0.176 1057 Planarity : 0.004 0.048 1142 Dihedral : 4.730 51.599 885 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.63 % Allowed : 28.37 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.30), residues: 832 helix: 2.16 (0.32), residues: 256 sheet: -0.46 (0.49), residues: 128 loop : -0.77 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 542 TYR 0.012 0.001 TYR C 725 PHE 0.010 0.001 PHE C 760 TRP 0.007 0.001 TRP A 442 HIS 0.006 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 6630) covalent geometry : angle 0.60479 ( 9021) SS BOND : bond 0.00671 ( 6) SS BOND : angle 1.30128 ( 12) hydrogen bonds : bond 0.03691 ( 244) hydrogen bonds : angle 4.12178 ( 735) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 57 time to evaluate : 0.237 Fit side-chains revert: symmetry clash REVERT: C 62 LEU cc_start: 0.7658 (OUTLIER) cc_final: 0.7253 (tt) REVERT: C 66 MET cc_start: 0.8851 (mpp) cc_final: 0.8548 (mpp) REVERT: C 83 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8534 (tt) REVERT: C 165 LEU cc_start: 0.8395 (OUTLIER) cc_final: 0.7930 (pp) REVERT: C 367 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8700 (tp) REVERT: C 381 LYS cc_start: 0.9280 (mttt) cc_final: 0.8975 (mtpp) REVERT: C 519 ILE cc_start: 0.7511 (OUTLIER) cc_final: 0.7118 (tp) REVERT: C 667 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8687 (tm) REVERT: C 725 TYR cc_start: 0.8642 (OUTLIER) cc_final: 0.7385 (m-80) REVERT: C 775 ILE cc_start: 0.6085 (OUTLIER) cc_final: 0.5851 (mp) REVERT: A 445 GLN cc_start: 0.7320 (tp40) cc_final: 0.6936 (tp40) REVERT: A 463 THR cc_start: 0.8836 (p) cc_final: 0.8540 (m) outliers start: 33 outliers final: 18 residues processed: 83 average time/residue: 0.0567 time to fit residues: 7.1029 Evaluate side-chains 84 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 58 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 667 LEU Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 0.4980 chunk 47 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.113761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.083951 restraints weight = 13359.357| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 3.30 r_work: 0.3202 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6636 Z= 0.168 Angle : 0.636 8.072 9033 Z= 0.310 Chirality : 0.044 0.171 1057 Planarity : 0.004 0.047 1142 Dihedral : 4.774 51.150 883 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 4.49 % Allowed : 28.09 % Favored : 67.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.32 (0.29), residues: 832 helix: 2.24 (0.32), residues: 249 sheet: -0.45 (0.49), residues: 128 loop : -0.76 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 542 TYR 0.013 0.001 TYR C 725 PHE 0.011 0.001 PHE A 518 TRP 0.009 0.001 TRP C 159 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 6630) covalent geometry : angle 0.63491 ( 9021) SS BOND : bond 0.00750 ( 6) SS BOND : angle 1.31986 ( 12) hydrogen bonds : bond 0.04042 ( 244) hydrogen bonds : angle 4.21444 ( 735) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 56 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: C 62 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7251 (tt) REVERT: C 66 MET cc_start: 0.8853 (mpp) cc_final: 0.8535 (mpp) REVERT: C 83 LEU cc_start: 0.8957 (OUTLIER) cc_final: 0.8601 (tt) REVERT: C 165 LEU cc_start: 0.8408 (OUTLIER) cc_final: 0.7963 (pp) REVERT: C 344 MET cc_start: 0.8767 (OUTLIER) cc_final: 0.8514 (mtm) REVERT: C 367 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8718 (tp) REVERT: C 381 LYS cc_start: 0.9320 (mttt) cc_final: 0.9008 (mtpp) REVERT: C 519 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7113 (tp) REVERT: C 725 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.7303 (m-80) REVERT: C 775 ILE cc_start: 0.6163 (OUTLIER) cc_final: 0.5930 (mp) REVERT: A 445 GLN cc_start: 0.7348 (tp40) cc_final: 0.6924 (tp40) REVERT: A 463 THR cc_start: 0.8798 (p) cc_final: 0.8427 (m) outliers start: 32 outliers final: 20 residues processed: 82 average time/residue: 0.0544 time to fit residues: 6.6840 Evaluate side-chains 84 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 618 CYS Chi-restraints excluded: chain C residue 637 MET Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 45 optimal weight: 0.0870 chunk 76 optimal weight: 6.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.114666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.084952 restraints weight = 13558.655| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 3.33 r_work: 0.3220 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6636 Z= 0.133 Angle : 0.627 9.140 9033 Z= 0.302 Chirality : 0.044 0.182 1057 Planarity : 0.004 0.048 1142 Dihedral : 4.683 50.501 883 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 4.49 % Allowed : 28.37 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.31 (0.29), residues: 832 helix: 2.26 (0.32), residues: 249 sheet: -0.52 (0.48), residues: 131 loop : -0.75 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 542 TYR 0.012 0.001 TYR C 725 PHE 0.011 0.001 PHE A 518 TRP 0.008 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 6630) covalent geometry : angle 0.62612 ( 9021) SS BOND : bond 0.00647 ( 6) SS BOND : angle 1.27750 ( 12) hydrogen bonds : bond 0.03766 ( 244) hydrogen bonds : angle 4.19037 ( 735) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 59 time to evaluate : 0.241 Fit side-chains REVERT: C 62 LEU cc_start: 0.7634 (OUTLIER) cc_final: 0.7240 (tt) REVERT: C 66 MET cc_start: 0.8807 (mpp) cc_final: 0.8522 (mpp) REVERT: C 83 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8528 (tt) REVERT: C 165 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.7939 (pp) REVERT: C 344 MET cc_start: 0.8751 (OUTLIER) cc_final: 0.8504 (mtm) REVERT: C 367 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8688 (tp) REVERT: C 381 LYS cc_start: 0.9279 (mttt) cc_final: 0.8980 (mtpp) REVERT: C 519 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7175 (tp) REVERT: C 721 MET cc_start: 0.8876 (ptp) cc_final: 0.8399 (ptp) REVERT: C 725 TYR cc_start: 0.8675 (OUTLIER) cc_final: 0.7298 (m-80) REVERT: C 775 ILE cc_start: 0.6201 (OUTLIER) cc_final: 0.5949 (mp) REVERT: A 445 GLN cc_start: 0.7319 (tp40) cc_final: 0.6876 (tp40) REVERT: A 463 THR cc_start: 0.8842 (p) cc_final: 0.8571 (m) outliers start: 32 outliers final: 20 residues processed: 85 average time/residue: 0.0544 time to fit residues: 6.9453 Evaluate side-chains 86 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 94 SER Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 65 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 21 optimal weight: 0.3980 chunk 50 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.114585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.084506 restraints weight = 13247.531| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 3.30 r_work: 0.3219 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6636 Z= 0.144 Angle : 0.636 9.027 9033 Z= 0.306 Chirality : 0.044 0.185 1057 Planarity : 0.004 0.049 1142 Dihedral : 4.702 50.112 883 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.07 % Allowed : 28.65 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.29), residues: 832 helix: 2.25 (0.32), residues: 249 sheet: -0.55 (0.49), residues: 129 loop : -0.78 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 542 TYR 0.012 0.001 TYR C 725 PHE 0.010 0.001 PHE A 518 TRP 0.007 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 6630) covalent geometry : angle 0.63456 ( 9021) SS BOND : bond 0.00682 ( 6) SS BOND : angle 1.28685 ( 12) hydrogen bonds : bond 0.03812 ( 244) hydrogen bonds : angle 4.18559 ( 735) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.164 Fit side-chains REVERT: C 62 LEU cc_start: 0.7598 (OUTLIER) cc_final: 0.7204 (tt) REVERT: C 66 MET cc_start: 0.8865 (mpp) cc_final: 0.8559 (mpp) REVERT: C 83 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8597 (tt) REVERT: C 165 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7959 (pp) REVERT: C 344 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.8516 (mtm) REVERT: C 367 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8697 (tp) REVERT: C 381 LYS cc_start: 0.9281 (mttt) cc_final: 0.8983 (mtpp) REVERT: C 519 ILE cc_start: 0.7563 (OUTLIER) cc_final: 0.7177 (tp) REVERT: C 721 MET cc_start: 0.8864 (ptp) cc_final: 0.8385 (ptp) REVERT: C 725 TYR cc_start: 0.8648 (OUTLIER) cc_final: 0.7230 (m-80) REVERT: C 775 ILE cc_start: 0.6235 (OUTLIER) cc_final: 0.5988 (mp) REVERT: A 445 GLN cc_start: 0.7268 (tp40) cc_final: 0.6872 (tp40) outliers start: 29 outliers final: 20 residues processed: 81 average time/residue: 0.0578 time to fit residues: 6.9825 Evaluate side-chains 84 residues out of total 732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 56 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 58 PHE Chi-restraints excluded: chain C residue 62 LEU Chi-restraints excluded: chain C residue 64 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 141 ILE Chi-restraints excluded: chain C residue 165 LEU Chi-restraints excluded: chain C residue 192 ILE Chi-restraints excluded: chain C residue 216 LEU Chi-restraints excluded: chain C residue 344 MET Chi-restraints excluded: chain C residue 367 LEU Chi-restraints excluded: chain C residue 389 ILE Chi-restraints excluded: chain C residue 519 ILE Chi-restraints excluded: chain C residue 560 ILE Chi-restraints excluded: chain C residue 561 LEU Chi-restraints excluded: chain C residue 640 THR Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 678 CYS Chi-restraints excluded: chain C residue 683 HIS Chi-restraints excluded: chain C residue 701 THR Chi-restraints excluded: chain C residue 725 TYR Chi-restraints excluded: chain C residue 768 PHE Chi-restraints excluded: chain C residue 775 ILE Chi-restraints excluded: chain C residue 792 LEU Chi-restraints excluded: chain C residue 815 LEU Chi-restraints excluded: chain A residue 439 CYS Chi-restraints excluded: chain A residue 519 SER Chi-restraints excluded: chain A residue 525 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 15 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 25 optimal weight: 0.2980 chunk 79 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 91 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 = 0.3875 r_free = 0.3875 target = 0.114980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.084807 restraints weight = 13330.822| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 3.34 r_work: 0.3224 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6636 Z= 0.132 Angle : 0.632 8.759 9033 Z= 0.305 Chirality : 0.044 0.183 1057 Planarity : 0.004 0.049 1142 Dihedral : 4.671 49.717 883 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 4.07 % Allowed : 29.07 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.30 (0.29), residues: 832 helix: 2.26 (0.32), residues: 249 sheet: -0.55 (0.48), residues: 131 loop : -0.76 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 542 TYR 0.011 0.001 TYR C 725 PHE 0.010 0.001 PHE A 518 TRP 0.010 0.001 TRP A 442 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6630) covalent geometry : angle 0.63066 ( 9021) SS BOND : bond 0.00651 ( 6) SS BOND : angle 1.26922 ( 12) hydrogen bonds : bond 0.03692 ( 244) hydrogen bonds : angle 4.15389 ( 735) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1548.17 seconds wall clock time: 27 minutes 17.87 seconds (1637.87 seconds total)