Starting phenix.real_space_refine on Wed Sep 17 07:11:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jh7_61474/09_2025/9jh7_61474.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jh7_61474/09_2025/9jh7_61474.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jh7_61474/09_2025/9jh7_61474.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jh7_61474/09_2025/9jh7_61474.map" model { file = "/net/cci-nas-00/data/ceres_data/9jh7_61474/09_2025/9jh7_61474.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jh7_61474/09_2025/9jh7_61474.cif" } resolution = 3.4 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= 0.010 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 P 15 5.49 5 S 20 5.16 5 C 4052 2.51 5 N 1047 2.21 5 O 1223 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: 6357 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 745, 6039 Classifications: {'peptide': 745} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 27, 'TRANS': 717} Chain: "C" Number of atoms: 318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 318 Classifications: {'DNA': 15} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 14} Time building chain proxies: 1.49, per 1000 atoms: 0.23 Number of scatterers: 6357 At special positions: 0 Unit cell: (77.08, 79.54, 106.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 P 15 15.00 O 1223 8.00 N 1047 7.00 C 4052 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 416.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1394 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 11 sheets defined 32.1% alpha, 19.3% beta 0 base pairs and 6 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 4.276A pdb=" N SER A 46 " --> pdb=" O LYS A 42 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N TYR A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 114 Processing helix chain 'A' and resid 187 through 194 Processing helix chain 'A' and resid 235 through 240 Processing helix chain 'A' and resid 241 through 248 removed outlier: 3.973A pdb=" N GLY A 244 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N TYR A 245 " --> pdb=" O ASN A 242 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS A 248 " --> pdb=" O TYR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.626A pdb=" N ASN A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 289 Processing helix chain 'A' and resid 289 through 301 removed outlier: 4.779A pdb=" N GLN A 298 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N LEU A 299 " --> pdb=" O GLU A 295 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LYS A 301 " --> pdb=" O GLU A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 319 Processing helix chain 'A' and resid 364 through 369 Processing helix chain 'A' and resid 388 through 405 Processing helix chain 'A' and resid 439 through 453 removed outlier: 3.564A pdb=" N TYR A 443 " --> pdb=" O ASP A 439 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N TYR A 453 " --> pdb=" O LYS A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 485 Processing helix chain 'A' and resid 494 through 502 Processing helix chain 'A' and resid 506 through 523 removed outlier: 4.203A pdb=" N TYR A 510 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ILE A 523 " --> pdb=" O ILE A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 584 through 602 Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.887A pdb=" N TYR A 624 " --> pdb=" O ASP A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 698 through 712 Processing helix chain 'A' and resid 723 through 735 Processing helix chain 'A' and resid 736 through 739 removed outlier: 3.672A pdb=" N ILE A 739 " --> pdb=" O ILE A 736 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 736 through 739' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 14 through 16 removed outlier: 3.750A pdb=" N ARG A 158 " --> pdb=" O SER A 135 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 14 through 16 removed outlier: 4.720A pdb=" N ASN A 155 " --> pdb=" O LYS A 148 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N LYS A 148 " --> pdb=" O ASN A 155 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA5, first strand: chain 'A' and resid 66 through 67 removed outlier: 3.730A pdb=" N LYS A 30 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 268 through 271 removed outlier: 3.819A pdb=" N TYR A 271 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 260 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ASN A 261 " --> pdb=" O GLU A 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 320 through 321 Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 346 removed outlier: 3.783A pdb=" N SER A 663 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N MET A 673 " --> pdb=" O LEU A 688 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE A 637 " --> pdb=" O SER A 693 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE A 609 " --> pdb=" O ASN A 636 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N ILE A 638 " --> pdb=" O ILE A 609 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N ILE A 611 " --> pdb=" O ILE A 638 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL A 640 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N ARG A 613 " --> pdb=" O VAL A 640 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER A 558 " --> pdb=" O GLY A 542 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 352 through 353 Processing sheet with id=AB1, first strand: chain 'A' and resid 432 through 435 removed outlier: 6.301A pdb=" N VAL A 382 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N TYR A 435 " --> pdb=" O VAL A 382 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N TYR A 384 " --> pdb=" O TYR A 435 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N LEU A 383 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 570 through 571 removed outlier: 4.091A pdb=" N TYR A 570 " --> pdb=" O ASP A 745 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ASP A 745 " --> pdb=" O TYR A 570 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 235 hydrogen bonds defined for protein. 660 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 6 stacking parallelities Total time for adding SS restraints: 1.21 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1727 1.33 - 1.45: 1247 1.45 - 1.57: 3482 1.57 - 1.69: 29 1.69 - 1.81: 35 Bond restraints: 6520 Sorted by residual: bond pdb=" N VAL A 378 " pdb=" CA VAL A 378 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.19e-02 7.06e+03 9.09e+00 bond pdb=" N GLU A 375 " pdb=" CA GLU A 375 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.23e+00 bond pdb=" C LEU A 682 " pdb=" N GLY A 683 " ideal model delta sigma weight residual 1.335 1.316 0.019 7.50e-03 1.78e+04 6.50e+00 bond pdb=" N LEU A 373 " pdb=" CA LEU A 373 " ideal model delta sigma weight residual 1.453 1.488 -0.036 1.50e-02 4.44e+03 5.63e+00 bond pdb=" N ARG A 379 " pdb=" CA ARG A 379 " ideal model delta sigma weight residual 1.459 1.488 -0.028 1.27e-02 6.20e+03 4.97e+00 ... (remaining 6515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 8207 1.83 - 3.66: 561 3.66 - 5.49: 62 5.49 - 7.31: 21 7.31 - 9.14: 6 Bond angle restraints: 8857 Sorted by residual: angle pdb=" N LYS A 88 " pdb=" CA LYS A 88 " pdb=" C LYS A 88 " ideal model delta sigma weight residual 110.35 118.59 -8.24 1.40e+00 5.10e-01 3.47e+01 angle pdb=" C VAL A 87 " pdb=" N LYS A 88 " pdb=" CA LYS A 88 " ideal model delta sigma weight residual 121.31 127.91 -6.60 1.49e+00 4.50e-01 1.96e+01 angle pdb=" C ASN A 258 " pdb=" N ILE A 259 " pdb=" CA ILE A 259 " ideal model delta sigma weight residual 121.97 129.73 -7.76 1.80e+00 3.09e-01 1.86e+01 angle pdb=" C GLY A 264 " pdb=" N ASN A 265 " pdb=" CA ASN A 265 " ideal model delta sigma weight residual 121.54 129.54 -8.00 1.91e+00 2.74e-01 1.75e+01 angle pdb=" C GLY A 742 " pdb=" N ARG A 743 " pdb=" CA ARG A 743 " ideal model delta sigma weight residual 121.54 128.98 -7.44 1.91e+00 2.74e-01 1.52e+01 ... (remaining 8852 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.96: 3738 25.96 - 51.93: 151 51.93 - 77.89: 17 77.89 - 103.85: 2 103.85 - 129.82: 1 Dihedral angle restraints: 3909 sinusoidal: 1722 harmonic: 2187 Sorted by residual: dihedral pdb=" CA PHE A 86 " pdb=" C PHE A 86 " pdb=" N VAL A 87 " pdb=" CA VAL A 87 " ideal model delta harmonic sigma weight residual 180.00 -142.46 -37.54 0 5.00e+00 4.00e-02 5.64e+01 dihedral pdb=" CA ASN A 258 " pdb=" C ASN A 258 " pdb=" N ILE A 259 " pdb=" CA ILE A 259 " ideal model delta harmonic sigma weight residual -180.00 -147.59 -32.41 0 5.00e+00 4.00e-02 4.20e+01 dihedral pdb=" CA ALA A 257 " pdb=" C ALA A 257 " pdb=" N ASN A 258 " pdb=" CA ASN A 258 " ideal model delta harmonic sigma weight residual -180.00 -148.00 -32.00 0 5.00e+00 4.00e-02 4.10e+01 ... (remaining 3906 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 643 0.050 - 0.100: 237 0.100 - 0.149: 64 0.149 - 0.199: 17 0.199 - 0.249: 3 Chirality restraints: 964 Sorted by residual: chirality pdb=" CB ILE A 582 " pdb=" CA ILE A 582 " pdb=" CG1 ILE A 582 " pdb=" CG2 ILE A 582 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CB VAL A 463 " pdb=" CA VAL A 463 " pdb=" CG1 VAL A 463 " pdb=" CG2 VAL A 463 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.18e+00 chirality pdb=" CG LEU A 383 " pdb=" CB LEU A 383 " pdb=" CD1 LEU A 383 " pdb=" CD2 LEU A 383 " both_signs ideal model delta sigma weight residual False -2.59 -2.79 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 961 not shown) Planarity restraints: 1071 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 728 " -0.004 2.00e-02 2.50e+03 1.87e-02 7.01e+00 pdb=" CG TYR A 728 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 728 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR A 728 " -0.025 2.00e-02 2.50e+03 pdb=" CE1 TYR A 728 " -0.016 2.00e-02 2.50e+03 pdb=" CE2 TYR A 728 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 728 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 728 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 463 " 0.041 5.00e-02 4.00e+02 6.14e-02 6.04e+00 pdb=" N PRO A 464 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 464 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 464 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 86 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.80e+00 pdb=" C PHE A 86 " -0.042 2.00e-02 2.50e+03 pdb=" O PHE A 86 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL A 87 " 0.014 2.00e-02 2.50e+03 ... (remaining 1068 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1773 2.80 - 3.33: 6087 3.33 - 3.85: 11128 3.85 - 4.38: 12737 4.38 - 4.90: 20674 Nonbonded interactions: 52399 Sorted by model distance: nonbonded pdb=" O LEU A 139 " pdb=" OH TYR A 306 " model vdw 2.278 3.040 nonbonded pdb=" NH1 ARG A 613 " pdb=" OE2 GLU A 639 " model vdw 2.312 3.120 nonbonded pdb=" O LYS A 50 " pdb=" OG SER A 53 " model vdw 2.321 3.040 nonbonded pdb=" OG SER A 650 " pdb=" OG1 THR A 657 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR A 125 " pdb=" OD2 ASP A 317 " model vdw 2.326 3.040 ... (remaining 52394 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: 1.530 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.320 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 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 : 0.007 0.052 6520 Z= 0.342 Angle : 1.022 9.143 8857 Z= 0.587 Chirality : 0.058 0.249 964 Planarity : 0.006 0.061 1071 Dihedral : 13.421 129.817 2515 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.75 % Favored : 91.12 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.42 % 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: -3.08 (0.27), residues: 743 helix: -2.27 (0.26), residues: 211 sheet: -1.60 (0.41), residues: 152 loop : -2.05 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 613 TYR 0.041 0.003 TYR A 728 PHE 0.028 0.003 PHE A 616 TRP 0.031 0.006 TRP A 623 HIS 0.024 0.005 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00693 ( 6520) covalent geometry : angle 1.02185 ( 8857) hydrogen bonds : bond 0.20452 ( 221) hydrogen bonds : angle 9.39035 ( 660) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 ASP cc_start: 0.9262 (m-30) cc_final: 0.8685 (p0) REVERT: A 112 LYS cc_start: 0.9592 (tppt) cc_final: 0.9168 (tptm) REVERT: A 167 ASN cc_start: 0.9484 (t0) cc_final: 0.8991 (t0) REVERT: A 176 LEU cc_start: 0.9394 (tp) cc_final: 0.9099 (tp) REVERT: A 191 MET cc_start: 0.9361 (mtp) cc_final: 0.9074 (mtm) REVERT: A 210 ILE cc_start: 0.8510 (mm) cc_final: 0.7962 (tp) REVERT: A 225 SER cc_start: 0.9551 (m) cc_final: 0.9085 (p) REVERT: A 226 GLU cc_start: 0.9183 (mm-30) cc_final: 0.8854 (mm-30) REVERT: A 253 GLU cc_start: 0.9060 (tm-30) cc_final: 0.8838 (tm-30) REVERT: A 259 ILE cc_start: 0.9635 (mt) cc_final: 0.9431 (mp) REVERT: A 269 TYR cc_start: 0.6193 (m-10) cc_final: 0.5830 (m-80) REVERT: A 289 ASP cc_start: 0.9051 (t0) cc_final: 0.8477 (t0) REVERT: A 295 GLU cc_start: 0.9766 (mm-30) cc_final: 0.9321 (tm-30) REVERT: A 296 ILE cc_start: 0.9869 (pt) cc_final: 0.9304 (pt) REVERT: A 304 MET cc_start: 0.9238 (mmt) cc_final: 0.8160 (mmp) REVERT: A 317 ASP cc_start: 0.8442 (m-30) cc_final: 0.8125 (m-30) REVERT: A 338 LYS cc_start: 0.9779 (mtpp) cc_final: 0.9546 (mmtm) REVERT: A 363 MET cc_start: 0.9008 (ttp) cc_final: 0.8619 (tmm) REVERT: A 364 GLN cc_start: 0.8859 (pt0) cc_final: 0.8624 (pt0) REVERT: A 444 LYS cc_start: 0.9644 (mttt) cc_final: 0.9329 (mttt) REVERT: A 453 TYR cc_start: 0.9178 (m-80) cc_final: 0.8835 (m-80) REVERT: A 495 LYS cc_start: 0.9679 (tttt) cc_final: 0.9357 (mtpp) REVERT: A 498 GLU cc_start: 0.9644 (mt-10) cc_final: 0.9421 (mt-10) REVERT: A 595 LEU cc_start: 0.9577 (mt) cc_final: 0.9285 (tp) REVERT: A 614 ASP cc_start: 0.9363 (t0) cc_final: 0.8786 (m-30) REVERT: A 626 ASN cc_start: 0.9809 (t0) cc_final: 0.9536 (p0) REVERT: A 639 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8422 (mm-30) REVERT: A 652 ASN cc_start: 0.9273 (t0) cc_final: 0.9042 (t0) REVERT: A 696 ASP cc_start: 0.9628 (t0) cc_final: 0.9413 (t0) REVERT: A 705 GLN cc_start: 0.8836 (mt0) cc_final: 0.8309 (mt0) REVERT: A 711 GLN cc_start: 0.9303 (mm-40) cc_final: 0.9028 (mm-40) outliers start: 0 outliers final: 0 residues processed: 215 average time/residue: 0.0957 time to fit residues: 26.3562 Evaluate side-chains 153 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 153 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0470 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 0.0020 chunk 51 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.0090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 39 ASN ** A 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN A 368 ASN A 490 GLN A 612 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.062927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.048724 restraints weight = 24913.925| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 6.79 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6520 Z= 0.170 Angle : 0.756 10.847 8857 Z= 0.403 Chirality : 0.049 0.192 964 Planarity : 0.005 0.045 1071 Dihedral : 14.396 131.154 974 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 16.68 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.08 % Favored : 91.79 % Rotamer: Outliers : 2.39 % Allowed : 12.86 % Favored : 84.75 % 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: -1.99 (0.30), residues: 743 helix: -0.86 (0.31), residues: 210 sheet: -1.21 (0.40), residues: 177 loop : -1.57 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 379 TYR 0.046 0.002 TYR A 554 PHE 0.027 0.002 PHE A 616 TRP 0.021 0.002 TRP A 623 HIS 0.024 0.004 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00366 ( 6520) covalent geometry : angle 0.75580 ( 8857) hydrogen bonds : bond 0.04664 ( 221) hydrogen bonds : angle 6.39715 ( 660) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 178 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 LYS cc_start: 0.9457 (mtmm) cc_final: 0.8978 (mmtt) REVERT: A 50 LYS cc_start: 0.9721 (mmtt) cc_final: 0.9251 (mttt) REVERT: A 58 LYS cc_start: 0.9400 (mmtt) cc_final: 0.9192 (mmmt) REVERT: A 71 GLU cc_start: 0.9362 (mm-30) cc_final: 0.8870 (pm20) REVERT: A 106 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8731 (tm-30) REVERT: A 112 LYS cc_start: 0.9577 (tppt) cc_final: 0.9195 (tptm) REVERT: A 149 LYS cc_start: 0.9180 (mtpp) cc_final: 0.8971 (mtpp) REVERT: A 167 ASN cc_start: 0.9462 (t0) cc_final: 0.9047 (t0) REVERT: A 176 LEU cc_start: 0.9251 (tp) cc_final: 0.8895 (tp) REVERT: A 181 ASP cc_start: 0.9369 (OUTLIER) cc_final: 0.8363 (p0) REVERT: A 191 MET cc_start: 0.9332 (mtp) cc_final: 0.9043 (mtm) REVERT: A 226 GLU cc_start: 0.9142 (mm-30) cc_final: 0.8877 (mm-30) REVERT: A 235 ILE cc_start: 0.9686 (pt) cc_final: 0.9305 (pt) REVERT: A 242 ASN cc_start: 0.9611 (m-40) cc_final: 0.9057 (p0) REVERT: A 243 GLN cc_start: 0.9571 (mt0) cc_final: 0.9313 (mt0) REVERT: A 289 ASP cc_start: 0.8987 (t0) cc_final: 0.8522 (t0) REVERT: A 295 GLU cc_start: 0.9762 (mm-30) cc_final: 0.9314 (tm-30) REVERT: A 304 MET cc_start: 0.9133 (mmt) cc_final: 0.8275 (mmm) REVERT: A 363 MET cc_start: 0.9022 (ttp) cc_final: 0.8562 (tmm) REVERT: A 364 GLN cc_start: 0.8933 (pt0) cc_final: 0.8679 (pt0) REVERT: A 444 LYS cc_start: 0.9669 (mttt) cc_final: 0.9352 (ptpp) REVERT: A 453 TYR cc_start: 0.9155 (m-80) cc_final: 0.8798 (m-80) REVERT: A 498 GLU cc_start: 0.9673 (mt-10) cc_final: 0.9463 (mt-10) REVERT: A 504 ARG cc_start: 0.9598 (tpm170) cc_final: 0.8768 (mmt180) REVERT: A 614 ASP cc_start: 0.9340 (t0) cc_final: 0.8747 (m-30) REVERT: A 626 ASN cc_start: 0.9728 (t0) cc_final: 0.9487 (p0) REVERT: A 640 VAL cc_start: 0.9590 (t) cc_final: 0.9098 (p) REVERT: A 673 MET cc_start: 0.8737 (ptp) cc_final: 0.8520 (ttp) REVERT: A 691 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8597 (mm-30) REVERT: A 696 ASP cc_start: 0.9674 (t0) cc_final: 0.9462 (t0) REVERT: A 705 GLN cc_start: 0.9281 (mt0) cc_final: 0.9014 (mm-40) REVERT: A 722 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8878 (tp) outliers start: 16 outliers final: 9 residues processed: 188 average time/residue: 0.0834 time to fit residues: 20.8698 Evaluate side-chains 154 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 143 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 586 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 722 LEU Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 73 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 61 optimal weight: 8.9990 chunk 58 optimal weight: 2.9990 chunk 53 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 490 GLN A 514 ASN A 574 ASN A 741 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.060487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.046857 restraints weight = 26350.371| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 6.54 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 6520 Z= 0.237 Angle : 0.730 6.005 8857 Z= 0.398 Chirality : 0.049 0.172 964 Planarity : 0.004 0.045 1071 Dihedral : 14.177 128.165 974 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 23.47 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.48 % Favored : 91.39 % Rotamer: Outliers : 4.19 % Allowed : 15.70 % Favored : 80.12 % 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: -1.76 (0.30), residues: 743 helix: -0.48 (0.31), residues: 216 sheet: -1.48 (0.39), residues: 162 loop : -1.36 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 618 TYR 0.034 0.002 TYR A 554 PHE 0.024 0.002 PHE A 388 TRP 0.014 0.002 TRP A 623 HIS 0.024 0.004 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 6520) covalent geometry : angle 0.72956 ( 8857) hydrogen bonds : bond 0.04409 ( 221) hydrogen bonds : angle 6.03937 ( 660) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9719 (mmtt) cc_final: 0.9298 (mttt) REVERT: A 106 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8817 (tm-30) REVERT: A 112 LYS cc_start: 0.9585 (tppt) cc_final: 0.9222 (tptm) REVERT: A 122 TYR cc_start: 0.8105 (t80) cc_final: 0.7805 (t80) REVERT: A 167 ASN cc_start: 0.9470 (t0) cc_final: 0.9024 (t0) REVERT: A 176 LEU cc_start: 0.9243 (tp) cc_final: 0.8888 (tp) REVERT: A 181 ASP cc_start: 0.9448 (OUTLIER) cc_final: 0.8564 (p0) REVERT: A 191 MET cc_start: 0.9309 (mtp) cc_final: 0.9021 (mtm) REVERT: A 225 SER cc_start: 0.9592 (m) cc_final: 0.9258 (p) REVERT: A 226 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8750 (mm-30) REVERT: A 242 ASN cc_start: 0.9620 (m-40) cc_final: 0.9399 (m110) REVERT: A 243 GLN cc_start: 0.9608 (mt0) cc_final: 0.9035 (pt0) REVERT: A 289 ASP cc_start: 0.9029 (t0) cc_final: 0.8558 (t0) REVERT: A 296 ILE cc_start: 0.9872 (pt) cc_final: 0.9537 (pp) REVERT: A 363 MET cc_start: 0.9139 (ttp) cc_final: 0.8742 (tmm) REVERT: A 407 LYS cc_start: 0.7093 (OUTLIER) cc_final: 0.6847 (tttt) REVERT: A 444 LYS cc_start: 0.9665 (mttt) cc_final: 0.9455 (mttt) REVERT: A 453 TYR cc_start: 0.9156 (m-80) cc_final: 0.8824 (m-80) REVERT: A 491 MET cc_start: 0.8815 (mpp) cc_final: 0.8582 (pmm) REVERT: A 495 LYS cc_start: 0.9832 (tttt) cc_final: 0.9507 (ttpp) REVERT: A 498 GLU cc_start: 0.9705 (mt-10) cc_final: 0.9467 (mt-10) REVERT: A 504 ARG cc_start: 0.9581 (tpm170) cc_final: 0.8732 (mmt180) REVERT: A 513 HIS cc_start: 0.9237 (m-70) cc_final: 0.8935 (m90) REVERT: A 533 MET cc_start: 0.7456 (tpt) cc_final: 0.6760 (tpt) REVERT: A 595 LEU cc_start: 0.9626 (mm) cc_final: 0.9269 (tp) REVERT: A 605 TYR cc_start: 0.9483 (m-80) cc_final: 0.9244 (m-10) REVERT: A 626 ASN cc_start: 0.9757 (t0) cc_final: 0.9498 (p0) REVERT: A 691 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8487 (mm-30) REVERT: A 692 LYS cc_start: 0.9467 (OUTLIER) cc_final: 0.9248 (ttmt) REVERT: A 703 LEU cc_start: 0.9580 (mt) cc_final: 0.9007 (tt) REVERT: A 730 ASP cc_start: 0.9601 (t0) cc_final: 0.9383 (t0) outliers start: 28 outliers final: 15 residues processed: 164 average time/residue: 0.0765 time to fit residues: 16.6885 Evaluate side-chains 150 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 132 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 673 MET Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 692 LYS Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 46 optimal weight: 1.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 58 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 10.0000 chunk 56 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 364 GLN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 574 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.063311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.049270 restraints weight = 25391.503| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 6.58 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6520 Z= 0.145 Angle : 0.687 7.790 8857 Z= 0.368 Chirality : 0.047 0.209 964 Planarity : 0.004 0.046 1071 Dihedral : 13.887 129.878 974 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 20.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.21 % Favored : 91.79 % Rotamer: Outliers : 2.99 % Allowed : 18.54 % Favored : 78.48 % 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: -1.52 (0.30), residues: 743 helix: -0.15 (0.32), residues: 217 sheet: -1.06 (0.43), residues: 144 loop : -1.46 (0.33), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 618 TYR 0.014 0.001 TYR A 107 PHE 0.016 0.002 PHE A 388 TRP 0.013 0.001 TRP A 623 HIS 0.023 0.003 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6520) covalent geometry : angle 0.68718 ( 8857) hydrogen bonds : bond 0.03733 ( 221) hydrogen bonds : angle 5.77972 ( 660) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 149 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9703 (mmtt) cc_final: 0.9262 (mttt) REVERT: A 106 GLU cc_start: 0.9026 (tm-30) cc_final: 0.8696 (tm-30) REVERT: A 112 LYS cc_start: 0.9531 (tppt) cc_final: 0.9094 (tptm) REVERT: A 122 TYR cc_start: 0.8026 (t80) cc_final: 0.7704 (t80) REVERT: A 167 ASN cc_start: 0.9453 (t0) cc_final: 0.9030 (t0) REVERT: A 176 LEU cc_start: 0.9264 (tp) cc_final: 0.8967 (tp) REVERT: A 181 ASP cc_start: 0.9458 (OUTLIER) cc_final: 0.8539 (p0) REVERT: A 225 SER cc_start: 0.9562 (m) cc_final: 0.9213 (p) REVERT: A 226 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8784 (mm-30) REVERT: A 243 GLN cc_start: 0.9591 (mt0) cc_final: 0.9048 (pt0) REVERT: A 289 ASP cc_start: 0.9118 (t0) cc_final: 0.8701 (t0) REVERT: A 298 GLN cc_start: 0.9211 (pm20) cc_final: 0.8941 (pp30) REVERT: A 363 MET cc_start: 0.9104 (ttp) cc_final: 0.8733 (tmm) REVERT: A 407 LYS cc_start: 0.6977 (OUTLIER) cc_final: 0.6745 (tttt) REVERT: A 444 LYS cc_start: 0.9673 (mttt) cc_final: 0.9386 (ptpp) REVERT: A 453 TYR cc_start: 0.9070 (m-80) cc_final: 0.8761 (m-80) REVERT: A 495 LYS cc_start: 0.9819 (tttt) cc_final: 0.9460 (ttpp) REVERT: A 517 LEU cc_start: 0.9754 (mt) cc_final: 0.9279 (tt) REVERT: A 595 LEU cc_start: 0.9597 (mm) cc_final: 0.9386 (tp) REVERT: A 625 GLU cc_start: 0.9358 (pt0) cc_final: 0.9082 (pp20) REVERT: A 691 GLU cc_start: 0.8816 (mt-10) cc_final: 0.8462 (mm-30) outliers start: 20 outliers final: 10 residues processed: 162 average time/residue: 0.0726 time to fit residues: 15.8027 Evaluate side-chains 147 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 135 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 44 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 407 LYS Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 674 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 64 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 41 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 14 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.059639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.045774 restraints weight = 26324.753| |-----------------------------------------------------------------------------| r_work (start): 0.2880 rms_B_bonded: 6.53 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6520 Z= 0.248 Angle : 0.748 8.778 8857 Z= 0.400 Chirality : 0.048 0.239 964 Planarity : 0.004 0.045 1071 Dihedral : 13.927 131.486 974 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 23.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 4.33 % Allowed : 19.13 % Favored : 76.53 % 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: -1.43 (0.31), residues: 743 helix: -0.21 (0.32), residues: 217 sheet: -1.33 (0.40), residues: 160 loop : -1.14 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 618 TYR 0.022 0.002 TYR A 554 PHE 0.018 0.002 PHE A 388 TRP 0.009 0.002 TRP A 623 HIS 0.029 0.004 HIS A 513 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 6520) covalent geometry : angle 0.74832 ( 8857) hydrogen bonds : bond 0.03842 ( 221) hydrogen bonds : angle 5.84488 ( 660) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9716 (mmtt) cc_final: 0.9304 (mttt) REVERT: A 106 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8690 (tm-30) REVERT: A 112 LYS cc_start: 0.9548 (tppt) cc_final: 0.9148 (tptm) REVERT: A 122 TYR cc_start: 0.8069 (t80) cc_final: 0.7716 (t80) REVERT: A 146 GLU cc_start: 0.9105 (tp30) cc_final: 0.8852 (tp30) REVERT: A 176 LEU cc_start: 0.9223 (tp) cc_final: 0.8910 (tp) REVERT: A 181 ASP cc_start: 0.9480 (OUTLIER) cc_final: 0.8564 (p0) REVERT: A 225 SER cc_start: 0.9587 (m) cc_final: 0.9246 (p) REVERT: A 226 GLU cc_start: 0.9109 (mm-30) cc_final: 0.8745 (mm-30) REVERT: A 242 ASN cc_start: 0.9649 (m-40) cc_final: 0.9378 (m110) REVERT: A 243 GLN cc_start: 0.9591 (mt0) cc_final: 0.8992 (pt0) REVERT: A 289 ASP cc_start: 0.9033 (t0) cc_final: 0.8571 (t0) REVERT: A 298 GLN cc_start: 0.9135 (pm20) cc_final: 0.8845 (pp30) REVERT: A 363 MET cc_start: 0.9147 (ttp) cc_final: 0.8811 (tmm) REVERT: A 453 TYR cc_start: 0.9094 (m-80) cc_final: 0.8761 (m-80) REVERT: A 495 LYS cc_start: 0.9812 (tttt) cc_final: 0.9585 (ttmm) REVERT: A 498 GLU cc_start: 0.9638 (mt-10) cc_final: 0.9296 (mp0) REVERT: A 504 ARG cc_start: 0.9591 (tpm170) cc_final: 0.8608 (mmt180) REVERT: A 595 LEU cc_start: 0.9636 (mm) cc_final: 0.9299 (pp) REVERT: A 625 GLU cc_start: 0.9391 (pt0) cc_final: 0.9136 (pp20) REVERT: A 646 LEU cc_start: 0.8707 (mp) cc_final: 0.8304 (tt) REVERT: A 691 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8479 (mm-30) REVERT: A 703 LEU cc_start: 0.9589 (mt) cc_final: 0.9201 (tt) outliers start: 29 outliers final: 22 residues processed: 157 average time/residue: 0.0770 time to fit residues: 16.1851 Evaluate side-chains 151 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 162 ILE Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 40 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 0.7980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 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 = 0.3237 r_free = 0.3237 target = 0.061734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.048064 restraints weight = 25893.286| |-----------------------------------------------------------------------------| r_work (start): 0.2920 rms_B_bonded: 6.49 r_work (final): 0.2920 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6520 Z= 0.158 Angle : 0.737 11.475 8857 Z= 0.386 Chirality : 0.047 0.250 964 Planarity : 0.004 0.045 1071 Dihedral : 13.841 131.592 974 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.69 % Allowed : 20.93 % Favored : 76.38 % 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: -1.33 (0.31), residues: 743 helix: 0.05 (0.32), residues: 217 sheet: -1.14 (0.41), residues: 149 loop : -1.27 (0.34), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 618 TYR 0.022 0.002 TYR A 554 PHE 0.017 0.002 PHE A 61 TRP 0.008 0.001 TRP A 623 HIS 0.006 0.001 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 6520) covalent geometry : angle 0.73670 ( 8857) hydrogen bonds : bond 0.03580 ( 221) hydrogen bonds : angle 5.75539 ( 660) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 136 time to evaluate : 0.293 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 LYS cc_start: 0.9691 (mmtt) cc_final: 0.9255 (mttt) REVERT: A 106 GLU cc_start: 0.8984 (tm-30) cc_final: 0.8664 (tm-30) REVERT: A 112 LYS cc_start: 0.9510 (tppt) cc_final: 0.9093 (tptp) REVERT: A 122 TYR cc_start: 0.8019 (t80) cc_final: 0.7668 (t80) REVERT: A 146 GLU cc_start: 0.9109 (tp30) cc_final: 0.8820 (tp30) REVERT: A 167 ASN cc_start: 0.9426 (t0) cc_final: 0.9014 (t0) REVERT: A 176 LEU cc_start: 0.9229 (tp) cc_final: 0.8905 (tp) REVERT: A 181 ASP cc_start: 0.9459 (OUTLIER) cc_final: 0.8504 (p0) REVERT: A 225 SER cc_start: 0.9580 (m) cc_final: 0.9221 (p) REVERT: A 226 GLU cc_start: 0.9135 (mm-30) cc_final: 0.8797 (mm-30) REVERT: A 243 GLN cc_start: 0.9561 (mt0) cc_final: 0.8954 (pt0) REVERT: A 289 ASP cc_start: 0.9109 (t0) cc_final: 0.8526 (t0) REVERT: A 298 GLN cc_start: 0.9138 (pm20) cc_final: 0.8853 (pp30) REVERT: A 363 MET cc_start: 0.9101 (ttp) cc_final: 0.8724 (tmm) REVERT: A 453 TYR cc_start: 0.9059 (m-80) cc_final: 0.8727 (m-80) REVERT: A 495 LYS cc_start: 0.9804 (tttt) cc_final: 0.9569 (ttmm) REVERT: A 498 GLU cc_start: 0.9607 (mt-10) cc_final: 0.9228 (mp0) REVERT: A 504 ARG cc_start: 0.9503 (tpm170) cc_final: 0.8559 (mmt180) REVERT: A 562 ASP cc_start: 0.8314 (t70) cc_final: 0.8090 (p0) REVERT: A 595 LEU cc_start: 0.9617 (mm) cc_final: 0.9247 (pp) REVERT: A 608 ASN cc_start: 0.9258 (m-40) cc_final: 0.8552 (t0) REVERT: A 625 GLU cc_start: 0.9336 (pt0) cc_final: 0.9090 (pp20) REVERT: A 691 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8479 (mm-30) outliers start: 18 outliers final: 15 residues processed: 148 average time/residue: 0.0741 time to fit residues: 15.0666 Evaluate side-chains 143 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 265 ASN Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 619 GLU Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 54 optimal weight: 0.2980 chunk 21 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 2.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 265 ASN ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.060411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.046432 restraints weight = 26374.695| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 6.62 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 6520 Z= 0.216 Angle : 0.766 13.419 8857 Z= 0.404 Chirality : 0.048 0.242 964 Planarity : 0.004 0.050 1071 Dihedral : 13.832 131.788 974 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 23.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.74 % Allowed : 21.23 % Favored : 75.04 % 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: -1.25 (0.31), residues: 743 helix: 0.10 (0.33), residues: 218 sheet: -1.20 (0.39), residues: 162 loop : -1.15 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 618 TYR 0.026 0.002 TYR A 554 PHE 0.015 0.002 PHE A 388 TRP 0.008 0.002 TRP A 623 HIS 0.007 0.002 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00463 ( 6520) covalent geometry : angle 0.76569 ( 8857) hydrogen bonds : bond 0.03678 ( 221) hydrogen bonds : angle 5.78880 ( 660) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 128 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 LYS cc_start: 0.9401 (OUTLIER) cc_final: 0.9133 (mttp) REVERT: A 106 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8724 (tm-30) REVERT: A 112 LYS cc_start: 0.9548 (tppt) cc_final: 0.9146 (tptm) REVERT: A 122 TYR cc_start: 0.8075 (t80) cc_final: 0.7737 (t80) REVERT: A 146 GLU cc_start: 0.9146 (tp30) cc_final: 0.8871 (tp30) REVERT: A 176 LEU cc_start: 0.9175 (tp) cc_final: 0.8868 (tp) REVERT: A 225 SER cc_start: 0.9615 (m) cc_final: 0.9279 (p) REVERT: A 226 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8795 (mm-30) REVERT: A 243 GLN cc_start: 0.9532 (mt0) cc_final: 0.8925 (pt0) REVERT: A 256 ASN cc_start: 0.9161 (t0) cc_final: 0.8739 (m-40) REVERT: A 289 ASP cc_start: 0.8981 (t0) cc_final: 0.8518 (t0) REVERT: A 363 MET cc_start: 0.9126 (ttp) cc_final: 0.8776 (tmm) REVERT: A 453 TYR cc_start: 0.9100 (m-80) cc_final: 0.8730 (m-80) REVERT: A 495 LYS cc_start: 0.9820 (tttt) cc_final: 0.9589 (ttmm) REVERT: A 498 GLU cc_start: 0.9612 (mt-10) cc_final: 0.9227 (mp0) REVERT: A 562 ASP cc_start: 0.8395 (t70) cc_final: 0.8097 (p0) REVERT: A 595 LEU cc_start: 0.9619 (mm) cc_final: 0.9247 (pp) REVERT: A 608 ASN cc_start: 0.9218 (m-40) cc_final: 0.8505 (t0) REVERT: A 646 LEU cc_start: 0.8640 (mp) cc_final: 0.8234 (tt) REVERT: A 691 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8536 (mm-30) REVERT: A 734 LYS cc_start: 0.9136 (ptpp) cc_final: 0.8876 (ptpp) outliers start: 25 outliers final: 20 residues processed: 144 average time/residue: 0.0776 time to fit residues: 15.2221 Evaluate side-chains 148 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 127 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 380 PHE Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 25 optimal weight: 10.0000 chunk 4 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.061557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.047514 restraints weight = 26334.144| |-----------------------------------------------------------------------------| r_work (start): 0.2873 rms_B_bonded: 6.65 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6520 Z= 0.184 Angle : 0.786 12.172 8857 Z= 0.407 Chirality : 0.049 0.244 964 Planarity : 0.004 0.047 1071 Dihedral : 13.781 131.918 974 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.44 % Allowed : 22.57 % Favored : 73.99 % 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: -1.32 (0.31), residues: 743 helix: -0.01 (0.33), residues: 218 sheet: -1.18 (0.39), residues: 163 loop : -1.19 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 618 TYR 0.021 0.002 TYR A 554 PHE 0.015 0.002 PHE A 366 TRP 0.007 0.001 TRP A 623 HIS 0.007 0.002 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 6520) covalent geometry : angle 0.78646 ( 8857) hydrogen bonds : bond 0.03585 ( 221) hydrogen bonds : angle 5.80258 ( 660) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 MET cc_start: 0.9789 (tpp) cc_final: 0.9309 (tpp) REVERT: A 54 LYS cc_start: 0.9389 (OUTLIER) cc_final: 0.9076 (mttt) REVERT: A 106 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8708 (tm-30) REVERT: A 112 LYS cc_start: 0.9544 (tppt) cc_final: 0.9143 (tptm) REVERT: A 122 TYR cc_start: 0.8055 (t80) cc_final: 0.7704 (t80) REVERT: A 146 GLU cc_start: 0.9152 (tp30) cc_final: 0.8888 (tp30) REVERT: A 167 ASN cc_start: 0.9425 (t0) cc_final: 0.9019 (t0) REVERT: A 176 LEU cc_start: 0.9173 (tp) cc_final: 0.8869 (tp) REVERT: A 225 SER cc_start: 0.9609 (m) cc_final: 0.9219 (p) REVERT: A 226 GLU cc_start: 0.9170 (mm-30) cc_final: 0.8831 (mm-30) REVERT: A 256 ASN cc_start: 0.9130 (t0) cc_final: 0.8718 (m-40) REVERT: A 289 ASP cc_start: 0.9050 (t0) cc_final: 0.8607 (t0) REVERT: A 363 MET cc_start: 0.9111 (ttp) cc_final: 0.8751 (tmm) REVERT: A 372 LYS cc_start: 0.9204 (tppt) cc_final: 0.8873 (tppt) REVERT: A 453 TYR cc_start: 0.9087 (m-80) cc_final: 0.8728 (m-80) REVERT: A 495 LYS cc_start: 0.9815 (tttt) cc_final: 0.9569 (ttmm) REVERT: A 498 GLU cc_start: 0.9596 (mt-10) cc_final: 0.9189 (mp0) REVERT: A 562 ASP cc_start: 0.8347 (t70) cc_final: 0.8066 (p0) REVERT: A 589 GLU cc_start: 0.9616 (tt0) cc_final: 0.9229 (tm-30) REVERT: A 595 LEU cc_start: 0.9617 (mm) cc_final: 0.9262 (pp) REVERT: A 608 ASN cc_start: 0.9162 (m-40) cc_final: 0.8441 (t0) REVERT: A 625 GLU cc_start: 0.9313 (pt0) cc_final: 0.9076 (pp20) REVERT: A 646 LEU cc_start: 0.8664 (mp) cc_final: 0.8240 (tt) REVERT: A 691 GLU cc_start: 0.8885 (mt-10) cc_final: 0.8509 (mm-30) REVERT: A 705 GLN cc_start: 0.9450 (mt0) cc_final: 0.9130 (mm-40) REVERT: A 734 LYS cc_start: 0.9109 (ptpp) cc_final: 0.8792 (ptpp) outliers start: 23 outliers final: 20 residues processed: 145 average time/residue: 0.0780 time to fit residues: 15.2614 Evaluate side-chains 149 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 54 LYS Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 739 ILE Chi-restraints excluded: chain A residue 744 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 74 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 53 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 35 optimal weight: 0.2980 chunk 68 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 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 = 0.3248 r_free = 0.3248 target = 0.062346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.048342 restraints weight = 26134.185| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 6.59 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 6520 Z= 0.157 Angle : 0.781 12.680 8857 Z= 0.400 Chirality : 0.048 0.250 964 Planarity : 0.004 0.048 1071 Dihedral : 13.726 131.407 974 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 3.59 % Allowed : 23.02 % Favored : 73.39 % 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: -1.27 (0.31), residues: 743 helix: 0.16 (0.34), residues: 217 sheet: -1.15 (0.39), residues: 163 loop : -1.24 (0.34), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 618 TYR 0.019 0.002 TYR A 554 PHE 0.016 0.002 PHE A 366 TRP 0.007 0.001 TRP A 623 HIS 0.006 0.002 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 6520) covalent geometry : angle 0.78108 ( 8857) hydrogen bonds : bond 0.03476 ( 221) hydrogen bonds : angle 5.74510 ( 660) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8697 (tm-30) REVERT: A 112 LYS cc_start: 0.9514 (tppt) cc_final: 0.9111 (tptm) REVERT: A 122 TYR cc_start: 0.8020 (t80) cc_final: 0.7661 (t80) REVERT: A 146 GLU cc_start: 0.9129 (tp30) cc_final: 0.8873 (tp30) REVERT: A 167 ASN cc_start: 0.9437 (t0) cc_final: 0.9016 (t0) REVERT: A 176 LEU cc_start: 0.9159 (tp) cc_final: 0.8836 (tp) REVERT: A 225 SER cc_start: 0.9602 (m) cc_final: 0.9196 (p) REVERT: A 226 GLU cc_start: 0.9189 (mm-30) cc_final: 0.8851 (mm-30) REVERT: A 256 ASN cc_start: 0.9082 (t0) cc_final: 0.8682 (m-40) REVERT: A 289 ASP cc_start: 0.9090 (t0) cc_final: 0.8637 (t0) REVERT: A 294 LYS cc_start: 0.9576 (ptpp) cc_final: 0.9346 (ptpp) REVERT: A 363 MET cc_start: 0.9103 (ttp) cc_final: 0.8677 (tmm) REVERT: A 368 ASN cc_start: 0.9255 (m-40) cc_final: 0.8920 (m110) REVERT: A 372 LYS cc_start: 0.9190 (tppt) cc_final: 0.8852 (tppt) REVERT: A 453 TYR cc_start: 0.9035 (m-80) cc_final: 0.8707 (m-80) REVERT: A 495 LYS cc_start: 0.9810 (tttt) cc_final: 0.9570 (ttmm) REVERT: A 498 GLU cc_start: 0.9595 (mt-10) cc_final: 0.9183 (mp0) REVERT: A 562 ASP cc_start: 0.8326 (t70) cc_final: 0.8014 (p0) REVERT: A 595 LEU cc_start: 0.9611 (mm) cc_final: 0.9258 (pp) REVERT: A 608 ASN cc_start: 0.9078 (m-40) cc_final: 0.8405 (t0) REVERT: A 625 GLU cc_start: 0.9318 (pt0) cc_final: 0.9069 (pp20) REVERT: A 652 ASN cc_start: 0.9352 (t0) cc_final: 0.9107 (t0) REVERT: A 705 GLN cc_start: 0.9461 (mt0) cc_final: 0.8783 (mp10) REVERT: A 734 LYS cc_start: 0.9112 (ptpp) cc_final: 0.8795 (ptpp) outliers start: 24 outliers final: 20 residues processed: 145 average time/residue: 0.0795 time to fit residues: 15.6224 Evaluate side-chains 148 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 128 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 739 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 13 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 46 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 21 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 713 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 = 0.3224 r_free = 0.3224 target = 0.061356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.047391 restraints weight = 26270.190| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 6.56 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 6520 Z= 0.198 Angle : 0.824 12.696 8857 Z= 0.420 Chirality : 0.049 0.244 964 Planarity : 0.004 0.047 1071 Dihedral : 13.729 132.097 974 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 23.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.59 % Allowed : 23.77 % Favored : 72.65 % 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: -1.29 (0.31), residues: 743 helix: 0.12 (0.33), residues: 218 sheet: -1.18 (0.39), residues: 163 loop : -1.24 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 618 TYR 0.023 0.002 TYR A 554 PHE 0.015 0.002 PHE A 366 TRP 0.008 0.001 TRP A 623 HIS 0.007 0.002 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 6520) covalent geometry : angle 0.82354 ( 8857) hydrogen bonds : bond 0.03532 ( 221) hydrogen bonds : angle 5.79163 ( 660) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1486 Ramachandran restraints generated. 743 Oldfield, 0 Emsley, 743 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 132 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8704 (tm-30) REVERT: A 112 LYS cc_start: 0.9537 (tppt) cc_final: 0.9136 (tptm) REVERT: A 122 TYR cc_start: 0.8018 (t80) cc_final: 0.7659 (t80) REVERT: A 146 GLU cc_start: 0.9141 (tp30) cc_final: 0.8889 (tp30) REVERT: A 149 LYS cc_start: 0.9060 (mtpp) cc_final: 0.8794 (mmmt) REVERT: A 167 ASN cc_start: 0.9427 (t0) cc_final: 0.9041 (t0) REVERT: A 176 LEU cc_start: 0.9179 (tp) cc_final: 0.8878 (tp) REVERT: A 225 SER cc_start: 0.9612 (m) cc_final: 0.9192 (p) REVERT: A 226 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8802 (mm-30) REVERT: A 256 ASN cc_start: 0.9136 (t0) cc_final: 0.8725 (m-40) REVERT: A 289 ASP cc_start: 0.9067 (t0) cc_final: 0.8580 (t0) REVERT: A 294 LYS cc_start: 0.9590 (ptpp) cc_final: 0.9375 (ptpp) REVERT: A 353 MET cc_start: 0.8741 (ppp) cc_final: 0.8501 (ppp) REVERT: A 363 MET cc_start: 0.9125 (ttp) cc_final: 0.8696 (tmm) REVERT: A 372 LYS cc_start: 0.9220 (tppt) cc_final: 0.8880 (tppt) REVERT: A 453 TYR cc_start: 0.9043 (m-80) cc_final: 0.8707 (m-80) REVERT: A 495 LYS cc_start: 0.9809 (tttt) cc_final: 0.9569 (ttmm) REVERT: A 498 GLU cc_start: 0.9594 (mt-10) cc_final: 0.9177 (mp0) REVERT: A 533 MET cc_start: 0.8363 (tpp) cc_final: 0.8126 (tpp) REVERT: A 589 GLU cc_start: 0.9605 (tt0) cc_final: 0.9244 (tm-30) REVERT: A 595 LEU cc_start: 0.9613 (mm) cc_final: 0.9252 (pp) REVERT: A 608 ASN cc_start: 0.9044 (m-40) cc_final: 0.8356 (t0) REVERT: A 652 ASN cc_start: 0.9372 (t0) cc_final: 0.9116 (t0) REVERT: A 691 GLU cc_start: 0.8839 (mt-10) cc_final: 0.8492 (mm-30) outliers start: 24 outliers final: 24 residues processed: 145 average time/residue: 0.0751 time to fit residues: 14.7920 Evaluate side-chains 150 residues out of total 669 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 126 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 VAL Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 181 ASP Chi-restraints excluded: chain A residue 373 LEU Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 491 MET Chi-restraints excluded: chain A residue 503 SER Chi-restraints excluded: chain A residue 529 VAL Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 539 CYS Chi-restraints excluded: chain A residue 543 LEU Chi-restraints excluded: chain A residue 545 VAL Chi-restraints excluded: chain A residue 558 SER Chi-restraints excluded: chain A residue 626 ASN Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 637 ILE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 648 ILE Chi-restraints excluded: chain A residue 674 VAL Chi-restraints excluded: chain A residue 712 ILE Chi-restraints excluded: chain A residue 726 THR Chi-restraints excluded: chain A residue 739 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 75 random chunks: chunk 19 optimal weight: 4.9990 chunk 70 optimal weight: 6.9990 chunk 42 optimal weight: 0.1980 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.2980 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 GLN ** A 713 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.065788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.051431 restraints weight = 26095.521| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 6.81 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 6520 Z= 0.140 Angle : 0.817 12.297 8857 Z= 0.412 Chirality : 0.049 0.250 964 Planarity : 0.004 0.048 1071 Dihedral : 13.686 131.031 974 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.08 % Favored : 91.92 % Rotamer: Outliers : 2.39 % Allowed : 24.81 % Favored : 72.80 % 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: -1.28 (0.31), residues: 743 helix: -0.00 (0.33), residues: 224 sheet: -1.05 (0.40), residues: 162 loop : -1.22 (0.34), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 618 TYR 0.014 0.001 TYR A 306 PHE 0.015 0.002 PHE A 366 TRP 0.008 0.001 TRP A 207 HIS 0.005 0.002 HIS A 553 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 6520) covalent geometry : angle 0.81685 ( 8857) hydrogen bonds : bond 0.03327 ( 221) hydrogen bonds : angle 5.77999 ( 660) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1257.75 seconds wall clock time: 22 minutes 38.94 seconds (1358.94 seconds total)