Starting phenix.real_space_refine on Wed Feb 4 20:25:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rhr_53974/02_2026/9rhr_53974_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rhr_53974/02_2026/9rhr_53974.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rhr_53974/02_2026/9rhr_53974.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rhr_53974/02_2026/9rhr_53974.map" model { file = "/net/cci-nas-00/data/ceres_data/9rhr_53974/02_2026/9rhr_53974_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rhr_53974/02_2026/9rhr_53974_neut.cif" } resolution = 2.4 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= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 19 5.16 5 C 4062 2.51 5 N 1090 2.21 5 O 1280 1.98 5 H 6025 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12476 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 12476 Number of conformers: 1 Conformer: "" Number of residues, atoms: 809, 12476 Classifications: {'peptide': 809} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 35, 'TRANS': 773} Time building chain proxies: 2.68, per 1000 atoms: 0.21 Number of scatterers: 12476 At special positions: 0 Unit cell: (93.73, 110.11, 95.55, 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 19 16.00 O 1280 8.00 N 1090 7.00 C 4062 6.00 H 6025 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 477 " - pdb=" SG CYS A 484 " distance=2.03 Simple disulfide: pdb=" SG CYS A 777 " - pdb=" SG CYS A 784 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.12 Conformation dependent library (CDL) restraints added in 459.6 milliseconds 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1478 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 7 sheets defined 9.4% alpha, 40.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 73 through 79 Processing helix chain 'A' and resid 87 through 93 removed outlier: 3.748A pdb=" N ASN A 92 " --> pdb=" O LEU A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.925A pdb=" N ASN A 126 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 147 Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 221 through 223 No H-bonds generated for 'chain 'A' and resid 221 through 223' Processing helix chain 'A' and resid 228 through 238 removed outlier: 4.637A pdb=" N GLU A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N GLU A 234 " --> pdb=" O VAL A 230 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLY A 238 " --> pdb=" O GLU A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 475 removed outlier: 4.389A pdb=" N GLY A 473 " --> pdb=" O ALA A 470 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL A 475 " --> pdb=" O ALA A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 577 Processing helix chain 'A' and resid 711 through 714 removed outlier: 4.451A pdb=" N GLU A 714 " --> pdb=" O ASN A 711 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 711 through 714' Processing helix chain 'A' and resid 727 through 729 No H-bonds generated for 'chain 'A' and resid 727 through 729' Processing helix chain 'A' and resid 781 through 787 Processing sheet with id=AA1, first strand: chain 'A' and resid 68 through 72 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'A' and resid 211 through 219 removed outlier: 6.898A pdb=" N ALA A 264 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 10.881A pdb=" N ASP A 289 " --> pdb=" O TYR A 325 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N TYR A 325 " --> pdb=" O ASP A 289 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU A 291 " --> pdb=" O LYS A 323 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLY A 339 " --> pdb=" O GLU A 366 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 411 through 427 current: chain 'A' and resid 435 through 437 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 435 through 437 current: chain 'A' and resid 500 through 514 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 500 through 514 current: chain 'A' and resid 522 through 524 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 522 through 524 current: chain 'A' and resid 538 through 540 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 538 through 540 current: chain 'A' and resid 557 through 567 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 557 through 567 current: chain 'A' and resid 630 through 652 removed outlier: 5.617A pdb=" N GLY A 664 " --> pdb=" O GLU A 643 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N PHE A 645 " --> pdb=" O ASN A 662 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ASN A 662 " --> pdb=" O PHE A 645 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG A 647 " --> pdb=" O MET A 660 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N MET A 660 " --> pdb=" O ARG A 647 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N THR A 649 " --> pdb=" O ARG A 658 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ARG A 658 " --> pdb=" O THR A 649 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N THR A 651 " --> pdb=" O SER A 656 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N SER A 656 " --> pdb=" O THR A 651 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 655 through 677 current: chain 'A' and resid 687 through 699 removed outlier: 6.936A pdb=" N GLN A 822 " --> pdb=" O VAL A 818 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 383 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 386 through 387 current: chain 'A' and resid 493 through 497 Processing sheet with id=AA5, first strand: chain 'A' and resid 464 through 465 Processing sheet with id=AA6, first strand: chain 'A' and resid 716 through 719 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 722 through 725 current: chain 'A' and resid 793 through 801 Processing sheet with id=AA7, first strand: chain 'A' and resid 838 through 843 removed outlier: 4.750A pdb=" N VAL A 838 " --> pdb=" O LYS A 854 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 852 " --> pdb=" O THR A 840 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N GLN A 842 " --> pdb=" O ILE A 850 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 850 " --> pdb=" O GLN A 842 " (cutoff:3.500A) 220 hydrogen bonds defined for protein. 579 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.88 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 1862 1.02 - 1.22: 4216 1.22 - 1.42: 3004 1.42 - 1.62: 3535 1.62 - 1.82: 34 Bond restraints: 12651 Sorted by residual: bond pdb=" N GLY A 786 " pdb=" H GLY A 786 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N SER A 221 " pdb=" H SER A 221 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" CZ PHE A 266 " pdb=" HZ PHE A 266 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 PHE A 741 " pdb=" HE1 PHE A 741 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CH2 TRP A 347 " pdb=" HH2 TRP A 347 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 12646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16639 1.81 - 3.62: 4337 3.62 - 5.42: 1012 5.42 - 7.23: 542 7.23 - 9.04: 77 Bond angle restraints: 22607 Sorted by residual: angle pdb=" CB HIS A 281 " pdb=" CG HIS A 281 " pdb=" CD2 HIS A 281 " ideal model delta sigma weight residual 131.20 124.79 6.41 1.30e+00 5.92e-01 2.43e+01 angle pdb=" CA THR A 193 " pdb=" CB THR A 193 " pdb=" OG1 THR A 193 " ideal model delta sigma weight residual 109.60 116.94 -7.34 1.50e+00 4.44e-01 2.39e+01 angle pdb=" C GLN A 244 " pdb=" N PRO A 245 " pdb=" CA PRO A 245 " ideal model delta sigma weight residual 119.19 124.31 -5.12 1.06e+00 8.90e-01 2.34e+01 angle pdb=" N ARG A 658 " pdb=" CA ARG A 658 " pdb=" C ARG A 658 " ideal model delta sigma weight residual 109.96 101.85 8.11 1.68e+00 3.54e-01 2.33e+01 angle pdb=" C VAL A 197 " pdb=" CA VAL A 197 " pdb=" CB VAL A 197 " ideal model delta sigma weight residual 111.23 116.09 -4.86 1.01e+00 9.80e-01 2.32e+01 ... (remaining 22602 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5489 17.99 - 35.98: 387 35.98 - 53.97: 128 53.97 - 71.95: 78 71.95 - 89.94: 17 Dihedral angle restraints: 6099 sinusoidal: 3200 harmonic: 2899 Sorted by residual: dihedral pdb=" CB CYS A 777 " pdb=" SG CYS A 777 " pdb=" SG CYS A 784 " pdb=" CB CYS A 784 " ideal model delta sinusoidal sigma weight residual -86.00 -158.75 72.75 1 1.00e+01 1.00e-02 6.75e+01 dihedral pdb=" CA TRP A 595 " pdb=" C TRP A 595 " pdb=" N THR A 596 " pdb=" CA THR A 596 " ideal model delta harmonic sigma weight residual -180.00 -151.31 -28.69 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA ASN A 735 " pdb=" C ASN A 735 " pdb=" N THR A 736 " pdb=" CA THR A 736 " ideal model delta harmonic sigma weight residual 180.00 151.52 28.48 0 5.00e+00 4.00e-02 3.24e+01 ... (remaining 6096 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 514 0.075 - 0.151: 272 0.151 - 0.226: 106 0.226 - 0.301: 24 0.301 - 0.377: 7 Chirality restraints: 923 Sorted by residual: chirality pdb=" CA ASP A 328 " pdb=" N ASP A 328 " pdb=" C ASP A 328 " pdb=" CB ASP A 328 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA LYS A 91 " pdb=" N LYS A 91 " pdb=" C LYS A 91 " pdb=" CB LYS A 91 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CB THR A 193 " pdb=" CA THR A 193 " pdb=" OG1 THR A 193 " pdb=" CG2 THR A 193 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.96e+00 ... (remaining 920 not shown) Planarity restraints: 1963 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 711 " 0.281 2.00e-02 2.50e+03 4.49e-01 3.02e+03 pdb=" CG ASN A 711 " -0.029 2.00e-02 2.50e+03 pdb=" OD1 ASN A 711 " -0.272 2.00e-02 2.50e+03 pdb=" ND2 ASN A 711 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 711 " -0.715 2.00e-02 2.50e+03 pdb="HD22 ASN A 711 " 0.737 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 171 " 0.307 2.00e-02 2.50e+03 3.48e-01 1.82e+03 pdb=" CG ASN A 171 " -0.024 2.00e-02 2.50e+03 pdb=" OD1 ASN A 171 " -0.296 2.00e-02 2.50e+03 pdb=" ND2 ASN A 171 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 171 " -0.515 2.00e-02 2.50e+03 pdb="HD22 ASN A 171 " 0.529 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 150 " -0.238 2.00e-02 2.50e+03 3.09e-01 1.43e+03 pdb=" CD GLN A 150 " 0.017 2.00e-02 2.50e+03 pdb=" OE1 GLN A 150 " 0.230 2.00e-02 2.50e+03 pdb=" NE2 GLN A 150 " -0.002 2.00e-02 2.50e+03 pdb="HE21 GLN A 150 " 0.477 2.00e-02 2.50e+03 pdb="HE22 GLN A 150 " -0.485 2.00e-02 2.50e+03 ... (remaining 1960 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 1238 2.20 - 2.80: 22895 2.80 - 3.40: 35533 3.40 - 4.00: 49177 4.00 - 4.60: 71012 Nonbonded interactions: 179855 Sorted by model distance: nonbonded pdb=" OE1 GLU A 173 " pdb=" HG SER A 253 " model vdw 1.596 2.450 nonbonded pdb=" HG SER A 307 " pdb=" OD2 ASP A 309 " model vdw 1.606 2.450 nonbonded pdb=" HG SER A 420 " pdb=" OD1 ASP A 446 " model vdw 1.613 2.450 nonbonded pdb=" OD2 ASP A 554 " pdb=" HG SER A 556 " model vdw 1.616 2.450 nonbonded pdb=" HG1 THR A 62 " pdb=" OE1 GLU A 523 " model vdw 1.620 2.450 ... (remaining 179850 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 4.560 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: 0.090 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.280 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7085 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 : 0.013 0.102 6628 Z= 0.754 Angle : 1.779 9.038 9009 Z= 1.189 Chirality : 0.104 0.377 923 Planarity : 0.013 0.129 1190 Dihedral : 14.068 89.943 2376 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % 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 are not related in a simple way. whole: -1.41 (0.28), residues: 807 helix: -3.73 (0.48), residues: 36 sheet: -0.63 (0.27), residues: 384 loop : -0.82 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 292 TYR 0.120 0.019 TYR A 802 PHE 0.080 0.014 PHE A 168 TRP 0.129 0.020 TRP A 860 HIS 0.023 0.005 HIS A 371 Details of bonding type rmsd covalent geometry : bond 0.01266 ( 6626) covalent geometry : angle 1.77879 ( 9005) SS BOND : bond 0.00144 ( 2) SS BOND : angle 1.27398 ( 4) hydrogen bonds : bond 0.13337 ( 220) hydrogen bonds : angle 9.09798 ( 579) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 MET cc_start: 0.8541 (mtm) cc_final: 0.7962 (mmt) REVERT: A 316 MET cc_start: 0.8261 (ttm) cc_final: 0.8050 (ttm) REVERT: A 550 ASP cc_start: 0.7373 (m-30) cc_final: 0.7035 (m-30) REVERT: A 667 GLU cc_start: 0.7505 (tt0) cc_final: 0.7165 (tm-30) REVERT: A 687 GLU cc_start: 0.8100 (pt0) cc_final: 0.7817 (pp20) outliers start: 0 outliers final: 1 residues processed: 197 average time/residue: 0.7826 time to fit residues: 164.6367 Evaluate side-chains 114 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 533 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN A 144 ASN A 166 GLN A 273 GLN A 428 ASN A 607 ASN A 743 ASN A 745 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.126742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.109871 restraints weight = 26602.716| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.38 r_work: 0.3633 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3512 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 6628 Z= 0.229 Angle : 0.640 5.283 9009 Z= 0.353 Chirality : 0.046 0.144 923 Planarity : 0.005 0.056 1190 Dihedral : 6.702 24.580 901 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.14 % Allowed : 14.25 % Favored : 83.62 % 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 are not related in a simple way. whole: -1.33 (0.28), residues: 807 helix: -3.22 (0.58), residues: 30 sheet: -0.97 (0.25), residues: 397 loop : -0.35 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 312 TYR 0.014 0.002 TYR A 706 PHE 0.016 0.002 PHE A 683 TRP 0.009 0.001 TRP A 755 HIS 0.009 0.002 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00499 ( 6626) covalent geometry : angle 0.64032 ( 9005) SS BOND : bond 0.00228 ( 2) SS BOND : angle 0.64481 ( 4) hydrogen bonds : bond 0.04125 ( 220) hydrogen bonds : angle 7.43535 ( 579) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 153 ASP cc_start: 0.8416 (m-30) cc_final: 0.8151 (m-30) REVERT: A 166 GLN cc_start: 0.8126 (mt0) cc_final: 0.7842 (mt0) REVERT: A 179 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7446 (mm-30) REVERT: A 202 MET cc_start: 0.8234 (mtm) cc_final: 0.7608 (mmt) REVERT: A 205 LYS cc_start: 0.8373 (mptt) cc_final: 0.8154 (mmtm) REVERT: A 256 PHE cc_start: 0.7492 (m-80) cc_final: 0.7018 (t80) REVERT: A 316 MET cc_start: 0.8494 (ttm) cc_final: 0.8252 (ttm) REVERT: A 345 MET cc_start: 0.7382 (tpt) cc_final: 0.7006 (tpp) REVERT: A 348 GLU cc_start: 0.7905 (tt0) cc_final: 0.7677 (tt0) REVERT: A 416 THR cc_start: 0.7885 (OUTLIER) cc_final: 0.7628 (m) REVERT: A 667 GLU cc_start: 0.7489 (tt0) cc_final: 0.7102 (tm-30) REVERT: A 687 GLU cc_start: 0.7850 (pt0) cc_final: 0.7568 (pp20) REVERT: A 714 GLU cc_start: 0.8279 (tp30) cc_final: 0.7512 (pm20) outliers start: 15 outliers final: 9 residues processed: 127 average time/residue: 0.8079 time to fit residues: 109.5237 Evaluate side-chains 107 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 313 MET Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 464 LEU Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 762 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 77 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 665 HIS A 743 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.123716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.106979 restraints weight = 26910.438| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 2.37 r_work: 0.3594 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6628 Z= 0.243 Angle : 0.604 4.635 9009 Z= 0.333 Chirality : 0.046 0.150 923 Planarity : 0.005 0.064 1190 Dihedral : 6.110 21.302 899 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.28 % Allowed : 16.81 % Favored : 79.91 % 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 are not related in a simple way. whole: -1.58 (0.28), residues: 807 helix: -3.16 (0.65), residues: 30 sheet: -1.19 (0.24), residues: 389 loop : -0.49 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 811 TYR 0.021 0.002 TYR A 283 PHE 0.017 0.002 PHE A 719 TRP 0.011 0.001 TRP A 860 HIS 0.010 0.002 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 6626) covalent geometry : angle 0.60421 ( 9005) SS BOND : bond 0.00818 ( 2) SS BOND : angle 0.78783 ( 4) hydrogen bonds : bond 0.03658 ( 220) hydrogen bonds : angle 7.16622 ( 579) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7634 (pp-130) cc_final: 0.7318 (pp-130) REVERT: A 91 LYS cc_start: 0.7710 (pttp) cc_final: 0.7397 (pmtt) REVERT: A 166 GLN cc_start: 0.8208 (mt0) cc_final: 0.7979 (mt0) REVERT: A 179 GLU cc_start: 0.7735 (OUTLIER) cc_final: 0.7412 (mt-10) REVERT: A 202 MET cc_start: 0.8299 (mtm) cc_final: 0.7708 (mmt) REVERT: A 252 TYR cc_start: 0.8624 (m-80) cc_final: 0.8057 (m-80) REVERT: A 256 PHE cc_start: 0.7481 (m-80) cc_final: 0.7087 (t80) REVERT: A 316 MET cc_start: 0.8516 (ttm) cc_final: 0.8305 (ttm) REVERT: A 416 THR cc_start: 0.7951 (OUTLIER) cc_final: 0.7708 (m) REVERT: A 626 ARG cc_start: 0.8021 (ttm170) cc_final: 0.7545 (mpt180) REVERT: A 667 GLU cc_start: 0.7379 (tt0) cc_final: 0.6857 (tm-30) REVERT: A 698 LYS cc_start: 0.8321 (tptt) cc_final: 0.7473 (ttpt) REVERT: A 713 ASP cc_start: 0.7514 (OUTLIER) cc_final: 0.7088 (m-30) outliers start: 23 outliers final: 8 residues processed: 115 average time/residue: 0.7425 time to fit residues: 91.5328 Evaluate side-chains 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 82 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 72 optimal weight: 0.3980 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 59 optimal weight: 0.0070 chunk 43 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.2980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 273 GLN A 344 ASN ** A 570 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.124590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.107897 restraints weight = 26562.185| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 2.40 r_work: 0.3608 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3487 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6628 Z= 0.175 Angle : 0.550 4.298 9009 Z= 0.299 Chirality : 0.045 0.143 923 Planarity : 0.004 0.064 1190 Dihedral : 5.767 20.616 899 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.99 % Allowed : 19.09 % Favored : 78.92 % 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 are not related in a simple way. whole: -1.71 (0.29), residues: 807 helix: -2.97 (0.64), residues: 36 sheet: -1.34 (0.25), residues: 385 loop : -0.49 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.011 0.001 TYR A 283 PHE 0.013 0.001 PHE A 719 TRP 0.008 0.001 TRP A 860 HIS 0.008 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6626) covalent geometry : angle 0.55020 ( 9005) SS BOND : bond 0.00286 ( 2) SS BOND : angle 0.65880 ( 4) hydrogen bonds : bond 0.03204 ( 220) hydrogen bonds : angle 6.95898 ( 579) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 0.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7540 (pp-130) cc_final: 0.7111 (pp-130) REVERT: A 166 GLN cc_start: 0.8226 (mt0) cc_final: 0.8001 (mt0) REVERT: A 179 GLU cc_start: 0.7769 (OUTLIER) cc_final: 0.7351 (mt-10) REVERT: A 202 MET cc_start: 0.8303 (mtm) cc_final: 0.7717 (mmt) REVERT: A 205 LYS cc_start: 0.8377 (mptt) cc_final: 0.8124 (mmtm) REVERT: A 252 TYR cc_start: 0.8637 (m-80) cc_final: 0.8140 (m-80) REVERT: A 256 PHE cc_start: 0.7401 (m-80) cc_final: 0.7010 (t80) REVERT: A 312 ARG cc_start: 0.8101 (ttm110) cc_final: 0.7802 (ttm110) REVERT: A 316 MET cc_start: 0.8474 (ttm) cc_final: 0.8265 (ttm) REVERT: A 345 MET cc_start: 0.7311 (tpt) cc_final: 0.6959 (tpp) REVERT: A 626 ARG cc_start: 0.8090 (ttm170) cc_final: 0.7647 (mtt90) REVERT: A 667 GLU cc_start: 0.7373 (tt0) cc_final: 0.6896 (tm-30) REVERT: A 698 LYS cc_start: 0.8361 (tptt) cc_final: 0.7471 (ttpt) REVERT: A 714 GLU cc_start: 0.8356 (tp30) cc_final: 0.7486 (pm20) REVERT: A 843 THR cc_start: 0.8285 (m) cc_final: 0.8074 (p) REVERT: A 861 LEU cc_start: 0.8612 (tp) cc_final: 0.8367 (tm) outliers start: 14 outliers final: 8 residues processed: 100 average time/residue: 0.7841 time to fit residues: 84.0591 Evaluate side-chains 94 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 517 MET Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 866 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 74 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.0980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 ASN A 570 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.123404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.106489 restraints weight = 26950.896| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.42 r_work: 0.3589 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3469 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.5155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 6628 Z= 0.212 Angle : 0.552 4.867 9009 Z= 0.301 Chirality : 0.045 0.143 923 Planarity : 0.004 0.063 1190 Dihedral : 5.645 20.864 899 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.42 % Allowed : 18.09 % Favored : 78.49 % 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 are not related in a simple way. whole: -1.77 (0.29), residues: 807 helix: -2.95 (0.66), residues: 36 sheet: -1.48 (0.26), residues: 367 loop : -0.49 (0.32), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 555 TYR 0.013 0.001 TYR A 283 PHE 0.014 0.001 PHE A 719 TRP 0.009 0.001 TRP A 860 HIS 0.009 0.002 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 6626) covalent geometry : angle 0.55162 ( 9005) SS BOND : bond 0.00253 ( 2) SS BOND : angle 0.81775 ( 4) hydrogen bonds : bond 0.03215 ( 220) hydrogen bonds : angle 6.89415 ( 579) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7532 (OUTLIER) cc_final: 0.6926 (ppp) REVERT: A 166 GLN cc_start: 0.8210 (mt0) cc_final: 0.7984 (mt0) REVERT: A 179 GLU cc_start: 0.7793 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: A 202 MET cc_start: 0.8343 (mtm) cc_final: 0.7759 (mmt) REVERT: A 205 LYS cc_start: 0.8396 (mptt) cc_final: 0.8122 (mmtm) REVERT: A 252 TYR cc_start: 0.8625 (m-80) cc_final: 0.8105 (m-80) REVERT: A 256 PHE cc_start: 0.7380 (m-80) cc_final: 0.7013 (t80) REVERT: A 316 MET cc_start: 0.8519 (ttm) cc_final: 0.8304 (ttm) REVERT: A 345 MET cc_start: 0.7357 (tpt) cc_final: 0.6973 (tpp) REVERT: A 416 THR cc_start: 0.7978 (OUTLIER) cc_final: 0.7759 (m) REVERT: A 626 ARG cc_start: 0.8065 (ttm170) cc_final: 0.7374 (mmt-90) REVERT: A 667 GLU cc_start: 0.7381 (tt0) cc_final: 0.6861 (tm-30) REVERT: A 698 LYS cc_start: 0.8327 (tptt) cc_final: 0.7395 (ttpt) REVERT: A 713 ASP cc_start: 0.7538 (OUTLIER) cc_final: 0.7159 (m-30) REVERT: A 714 GLU cc_start: 0.8301 (tp30) cc_final: 0.7427 (pm20) REVERT: A 861 LEU cc_start: 0.8546 (tp) cc_final: 0.8294 (tm) outliers start: 24 outliers final: 10 residues processed: 108 average time/residue: 0.8436 time to fit residues: 96.6609 Evaluate side-chains 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 866 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 0.3980 chunk 76 optimal weight: 0.9990 chunk 56 optimal weight: 0.4980 chunk 42 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.122129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.105275 restraints weight = 26580.956| |-----------------------------------------------------------------------------| r_work (start): 0.3665 rms_B_bonded: 2.37 r_work: 0.3575 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3456 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.5361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 6628 Z= 0.247 Angle : 0.566 4.718 9009 Z= 0.309 Chirality : 0.045 0.144 923 Planarity : 0.004 0.063 1190 Dihedral : 5.640 21.685 899 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.99 % Allowed : 18.95 % Favored : 78.06 % 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 are not related in a simple way. whole: -1.92 (0.29), residues: 807 helix: -3.05 (0.66), residues: 36 sheet: -1.62 (0.26), residues: 368 loop : -0.54 (0.32), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 312 TYR 0.012 0.002 TYR A 283 PHE 0.015 0.002 PHE A 719 TRP 0.009 0.001 TRP A 860 HIS 0.009 0.002 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 6626) covalent geometry : angle 0.56628 ( 9005) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.91465 ( 4) hydrogen bonds : bond 0.03241 ( 220) hydrogen bonds : angle 6.96869 ( 579) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7392 (ppp) REVERT: A 166 GLN cc_start: 0.8257 (mt0) cc_final: 0.8015 (mt0) REVERT: A 179 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7496 (mp0) REVERT: A 202 MET cc_start: 0.8357 (mtm) cc_final: 0.7797 (mmt) REVERT: A 205 LYS cc_start: 0.8393 (mptt) cc_final: 0.8070 (mmtm) REVERT: A 252 TYR cc_start: 0.8677 (m-80) cc_final: 0.8150 (m-80) REVERT: A 256 PHE cc_start: 0.7407 (m-80) cc_final: 0.7065 (t80) REVERT: A 345 MET cc_start: 0.7386 (tpt) cc_final: 0.6998 (tpp) REVERT: A 626 ARG cc_start: 0.8022 (OUTLIER) cc_final: 0.7629 (mpt180) REVERT: A 667 GLU cc_start: 0.7425 (tt0) cc_final: 0.6930 (tm-30) REVERT: A 698 LYS cc_start: 0.8392 (tptt) cc_final: 0.7515 (ttpt) REVERT: A 713 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: A 714 GLU cc_start: 0.8281 (tp30) cc_final: 0.7512 (pm20) REVERT: A 861 LEU cc_start: 0.8591 (tp) cc_final: 0.8357 (tm) outliers start: 21 outliers final: 13 residues processed: 93 average time/residue: 0.7771 time to fit residues: 77.4610 Evaluate side-chains 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 866 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN A 858 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.121507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.104429 restraints weight = 26827.971| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.38 r_work: 0.3554 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 6628 Z= 0.295 Angle : 0.596 6.650 9009 Z= 0.325 Chirality : 0.046 0.146 923 Planarity : 0.005 0.061 1190 Dihedral : 5.719 22.622 899 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.13 % Allowed : 18.66 % Favored : 77.21 % 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 are not related in a simple way. whole: -2.16 (0.29), residues: 807 helix: -3.25 (0.63), residues: 36 sheet: -1.83 (0.25), residues: 369 loop : -0.63 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 555 TYR 0.013 0.002 TYR A 615 PHE 0.015 0.002 PHE A 719 TRP 0.009 0.001 TRP A 860 HIS 0.009 0.002 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00646 ( 6626) covalent geometry : angle 0.59530 ( 9005) SS BOND : bond 0.00147 ( 2) SS BOND : angle 0.99862 ( 4) hydrogen bonds : bond 0.03368 ( 220) hydrogen bonds : angle 7.04587 ( 579) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 75 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: A 68 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7400 (ppp) REVERT: A 166 GLN cc_start: 0.8287 (mt0) cc_final: 0.8036 (mt0) REVERT: A 179 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7527 (mp0) REVERT: A 202 MET cc_start: 0.8386 (mtm) cc_final: 0.7824 (mmt) REVERT: A 205 LYS cc_start: 0.8402 (mptt) cc_final: 0.8162 (mmtm) REVERT: A 252 TYR cc_start: 0.8668 (m-80) cc_final: 0.8212 (m-80) REVERT: A 256 PHE cc_start: 0.7443 (m-80) cc_final: 0.7120 (t80) REVERT: A 345 MET cc_start: 0.7387 (tpt) cc_final: 0.7015 (tpp) REVERT: A 558 ARG cc_start: 0.8024 (ptp-170) cc_final: 0.7683 (ptt-90) REVERT: A 577 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8435 (mtp180) REVERT: A 626 ARG cc_start: 0.8083 (OUTLIER) cc_final: 0.7680 (mpt180) REVERT: A 667 GLU cc_start: 0.7452 (tt0) cc_final: 0.6892 (tm-30) REVERT: A 685 PHE cc_start: 0.7080 (OUTLIER) cc_final: 0.6685 (m-10) REVERT: A 713 ASP cc_start: 0.7584 (OUTLIER) cc_final: 0.7265 (m-30) REVERT: A 714 GLU cc_start: 0.8286 (tp30) cc_final: 0.7601 (pm20) REVERT: A 829 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7889 (m-30) REVERT: A 861 LEU cc_start: 0.8593 (tp) cc_final: 0.8342 (tm) outliers start: 29 outliers final: 15 residues processed: 95 average time/residue: 0.9496 time to fit residues: 95.9850 Evaluate side-chains 93 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 370 GLU Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 577 ARG Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 619 LEU Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 685 PHE Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 829 ASP Chi-restraints excluded: chain A residue 866 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 chunk 68 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 67 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.123312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.106617 restraints weight = 26433.115| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.35 r_work: 0.3587 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3470 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6628 Z= 0.180 Angle : 0.547 6.165 9009 Z= 0.296 Chirality : 0.045 0.145 923 Planarity : 0.004 0.058 1190 Dihedral : 5.472 21.993 899 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.85 % Allowed : 19.23 % Favored : 77.92 % 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 are not related in a simple way. whole: -1.97 (0.29), residues: 807 helix: -3.14 (0.64), residues: 36 sheet: -1.74 (0.26), residues: 361 loop : -0.49 (0.32), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 555 TYR 0.012 0.001 TYR A 283 PHE 0.013 0.001 PHE A 441 TRP 0.010 0.001 TRP A 860 HIS 0.007 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 6626) covalent geometry : angle 0.54658 ( 9005) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.87700 ( 4) hydrogen bonds : bond 0.03017 ( 220) hydrogen bonds : angle 6.84392 ( 579) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7365 (ppp) REVERT: A 166 GLN cc_start: 0.8251 (mt0) cc_final: 0.7922 (mt0) REVERT: A 179 GLU cc_start: 0.7908 (OUTLIER) cc_final: 0.7497 (mp0) REVERT: A 202 MET cc_start: 0.8425 (mtm) cc_final: 0.7845 (mmt) REVERT: A 205 LYS cc_start: 0.8397 (mptt) cc_final: 0.8139 (mmtm) REVERT: A 252 TYR cc_start: 0.8644 (m-80) cc_final: 0.8127 (m-80) REVERT: A 256 PHE cc_start: 0.7381 (m-80) cc_final: 0.7077 (t80) REVERT: A 345 MET cc_start: 0.7378 (tpt) cc_final: 0.7002 (tpp) REVERT: A 558 ARG cc_start: 0.7931 (ptp-170) cc_final: 0.7612 (ptt-90) REVERT: A 626 ARG cc_start: 0.8039 (OUTLIER) cc_final: 0.7480 (mmt90) REVERT: A 667 GLU cc_start: 0.7334 (tt0) cc_final: 0.6827 (tm-30) REVERT: A 713 ASP cc_start: 0.7613 (OUTLIER) cc_final: 0.7299 (m-30) REVERT: A 714 GLU cc_start: 0.8313 (tp30) cc_final: 0.7552 (pm20) REVERT: A 861 LEU cc_start: 0.8478 (tp) cc_final: 0.8241 (tm) outliers start: 20 outliers final: 12 residues processed: 91 average time/residue: 0.8636 time to fit residues: 84.5610 Evaluate side-chains 88 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 866 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 55 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 20 optimal weight: 0.4980 chunk 54 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 5 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.123161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.106637 restraints weight = 26438.212| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.35 r_work: 0.3592 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.5692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6628 Z= 0.171 Angle : 0.539 7.006 9009 Z= 0.290 Chirality : 0.044 0.142 923 Planarity : 0.004 0.056 1190 Dihedral : 5.334 21.593 899 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.14 % Allowed : 20.09 % Favored : 77.78 % 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 are not related in a simple way. whole: -1.82 (0.30), residues: 807 helix: -3.06 (0.65), residues: 36 sheet: -1.72 (0.26), residues: 369 loop : -0.27 (0.33), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 216 TYR 0.012 0.001 TYR A 283 PHE 0.011 0.001 PHE A 441 TRP 0.013 0.001 TRP A 353 HIS 0.007 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 6626) covalent geometry : angle 0.53810 ( 9005) SS BOND : bond 0.00097 ( 2) SS BOND : angle 1.18711 ( 4) hydrogen bonds : bond 0.02917 ( 220) hydrogen bonds : angle 6.71828 ( 579) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7764 (OUTLIER) cc_final: 0.7435 (ppp) REVERT: A 166 GLN cc_start: 0.8255 (mt0) cc_final: 0.7948 (mt0) REVERT: A 179 GLU cc_start: 0.7912 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: A 202 MET cc_start: 0.8414 (mtm) cc_final: 0.7854 (mmt) REVERT: A 205 LYS cc_start: 0.8392 (mptt) cc_final: 0.8118 (mmtm) REVERT: A 252 TYR cc_start: 0.8633 (m-80) cc_final: 0.8170 (m-80) REVERT: A 256 PHE cc_start: 0.7402 (m-80) cc_final: 0.7083 (t80) REVERT: A 270 TYR cc_start: 0.8838 (t80) cc_final: 0.8587 (t80) REVERT: A 345 MET cc_start: 0.7350 (tpt) cc_final: 0.6978 (tpp) REVERT: A 558 ARG cc_start: 0.7872 (ptp-170) cc_final: 0.7577 (ptt-90) REVERT: A 626 ARG cc_start: 0.8037 (OUTLIER) cc_final: 0.7455 (mmt90) REVERT: A 713 ASP cc_start: 0.7591 (OUTLIER) cc_final: 0.7281 (m-30) REVERT: A 714 GLU cc_start: 0.8242 (tp30) cc_final: 0.7481 (pm20) REVERT: A 861 LEU cc_start: 0.8470 (tp) cc_final: 0.8237 (tm) outliers start: 15 outliers final: 11 residues processed: 85 average time/residue: 0.8051 time to fit residues: 73.5588 Evaluate side-chains 86 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 866 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 44 optimal weight: 0.0170 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 69 optimal weight: 0.1980 chunk 54 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.122839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.106238 restraints weight = 26659.194| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.38 r_work: 0.3583 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.5758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 6628 Z= 0.190 Angle : 0.547 9.351 9009 Z= 0.294 Chirality : 0.045 0.142 923 Planarity : 0.004 0.056 1190 Dihedral : 5.324 21.698 899 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.56 % Allowed : 19.66 % Favored : 77.78 % 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 are not related in a simple way. whole: -1.87 (0.30), residues: 807 helix: -3.06 (0.66), residues: 36 sheet: -1.78 (0.26), residues: 371 loop : -0.26 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 555 TYR 0.012 0.001 TYR A 283 PHE 0.013 0.001 PHE A 441 TRP 0.015 0.001 TRP A 353 HIS 0.008 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 6626) covalent geometry : angle 0.54694 ( 9005) SS BOND : bond 0.00154 ( 2) SS BOND : angle 1.16841 ( 4) hydrogen bonds : bond 0.02954 ( 220) hydrogen bonds : angle 6.69845 ( 579) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1614 Ramachandran restraints generated. 807 Oldfield, 0 Emsley, 807 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 MET cc_start: 0.7762 (OUTLIER) cc_final: 0.7429 (ppp) REVERT: A 166 GLN cc_start: 0.8260 (mt0) cc_final: 0.7950 (mt0) REVERT: A 179 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7484 (mp0) REVERT: A 202 MET cc_start: 0.8438 (mtm) cc_final: 0.7895 (mmt) REVERT: A 205 LYS cc_start: 0.8382 (mptt) cc_final: 0.8103 (mmtm) REVERT: A 252 TYR cc_start: 0.8614 (m-80) cc_final: 0.8152 (m-80) REVERT: A 256 PHE cc_start: 0.7389 (m-80) cc_final: 0.7086 (t80) REVERT: A 270 TYR cc_start: 0.8847 (t80) cc_final: 0.8561 (t80) REVERT: A 345 MET cc_start: 0.7368 (tpt) cc_final: 0.6993 (tpp) REVERT: A 558 ARG cc_start: 0.7880 (ptp-170) cc_final: 0.7589 (ptt-90) REVERT: A 626 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7476 (mmt90) REVERT: A 667 GLU cc_start: 0.7355 (tt0) cc_final: 0.6774 (tm-30) REVERT: A 713 ASP cc_start: 0.7525 (OUTLIER) cc_final: 0.7212 (m-30) REVERT: A 714 GLU cc_start: 0.8297 (tp30) cc_final: 0.7536 (pm20) REVERT: A 861 LEU cc_start: 0.8420 (tp) cc_final: 0.8195 (tm) outliers start: 18 outliers final: 13 residues processed: 86 average time/residue: 0.7870 time to fit residues: 72.9602 Evaluate side-chains 87 residues out of total 702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 179 GLU Chi-restraints excluded: chain A residue 206 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 352 SER Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 596 THR Chi-restraints excluded: chain A residue 601 ARG Chi-restraints excluded: chain A residue 626 ARG Chi-restraints excluded: chain A residue 679 SER Chi-restraints excluded: chain A residue 709 SER Chi-restraints excluded: chain A residue 713 ASP Chi-restraints excluded: chain A residue 756 ASP Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain A residue 866 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 79 optimal weight: 0.0770 chunk 66 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 26 optimal weight: 0.0970 chunk 72 optimal weight: 0.5980 chunk 40 optimal weight: 0.6980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 665 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 = 0.3891 r_free = 0.3891 target = 0.124330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.107634 restraints weight = 26562.759| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.39 r_work: 0.3600 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3484 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.5826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6628 Z= 0.153 Angle : 0.532 7.998 9009 Z= 0.285 Chirality : 0.044 0.141 923 Planarity : 0.004 0.055 1190 Dihedral : 5.183 21.143 899 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.99 % Allowed : 20.66 % Favored : 77.35 % 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 are not related in a simple way. whole: -1.81 (0.30), residues: 807 helix: -2.92 (0.67), residues: 36 sheet: -1.75 (0.26), residues: 371 loop : -0.21 (0.33), residues: 400 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 342 TYR 0.011 0.001 TYR A 283 PHE 0.011 0.001 PHE A 441 TRP 0.027 0.001 TRP A 353 HIS 0.009 0.001 HIS A 665 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6626) covalent geometry : angle 0.53139 ( 9005) SS BOND : bond 0.00096 ( 2) SS BOND : angle 1.13989 ( 4) hydrogen bonds : bond 0.02848 ( 220) hydrogen bonds : angle 6.57926 ( 579) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5237.68 seconds wall clock time: 89 minutes 20.22 seconds (5360.22 seconds total)