Starting phenix.real_space_refine on Wed Feb 4 10:40:51 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i0o_52563/02_2026/9i0o_52563_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i0o_52563/02_2026/9i0o_52563.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i0o_52563/02_2026/9i0o_52563.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i0o_52563/02_2026/9i0o_52563.map" model { file = "/net/cci-nas-00/data/ceres_data/9i0o_52563/02_2026/9i0o_52563_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i0o_52563/02_2026/9i0o_52563_trim.cif" } resolution = 3.36 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= 0.001 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 25 5.16 5 C 3183 2.51 5 N 842 2.21 5 O 1004 1.98 5 H 4754 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 9808 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 9511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 621, 9511 Classifications: {'peptide': 621} Link IDs: {'PTRANS': 21, 'TRANS': 599} Chain breaks: 2 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "B" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 227 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.69, per 1000 atoms: 0.17 Number of scatterers: 9808 At special positions: 0 Unit cell: (65.076, 94.248, 94.248, 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 25 16.00 O 1004 8.00 N 842 7.00 C 3183 6.00 H 4754 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 224 " - pdb=" SG CYS A 244 " distance=2.03 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 579 " - pdb=" SG CYS A 618 " distance=2.03 Simple disulfide: pdb=" SG CYS A 601 " - pdb=" SG CYS A 633 " distance=2.03 Simple disulfide: pdb=" SG CYS A 635 " - pdb=" SG CYS A 690 " distance=2.03 Simple disulfide: pdb=" SG CYS A 642 " - pdb=" SG CYS A 655 " 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 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " NAG-ASN " NAG A 801 " - " ASN A 129 " " NAG C 1 " - " ASN A 373 " " NAG D 1 " - " ASN A 549 " Time building additional restraints: 0.87 Conformation dependent library (CDL) restraints added in 187.1 milliseconds 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 13 sheets defined 3.8% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A' and resid 58 through 66 removed outlier: 4.042A pdb=" N LYS A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 129 Processing helix chain 'A' and resid 431 through 437 Processing helix chain 'A' and resid 636 through 638 No H-bonds generated for 'chain 'A' and resid 636 through 638' Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 72 removed outlier: 3.681A pdb=" N PHE A 72 " --> pdb=" O TRP A 564 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TRP A 564 " --> pdb=" O PHE A 72 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLY A 554 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N GLY A 538 " --> pdb=" O TRP A 553 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N PHE A 555 " --> pdb=" O PHE A 536 " (cutoff:3.500A) removed outlier: 5.700A pdb=" N PHE A 536 " --> pdb=" O PHE A 555 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 122 through 123 removed outlier: 4.548A pdb=" N VAL A 90 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL A 79 " --> pdb=" O TYR B 18 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS B 16 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 190 removed outlier: 5.857A pdb=" N TYR A 196 " --> pdb=" O SER A 190 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N LEU A 206 " --> pdb=" O ILE A 219 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 228 removed outlier: 6.725A pdb=" N THR A 237 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ALA A 226 " --> pdb=" O PHE A 235 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N PHE A 235 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N LEU A 251 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N VAL A 268 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N LEU A 253 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS A 269 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER A 283 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N PHE A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE A 281 " --> pdb=" O PHE A 273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 323 removed outlier: 7.022A pdb=" N TYR A 318 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N ASP A 333 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE A 320 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N HIS A 331 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N ALA A 322 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY A 341 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ASP A 358 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N ILE A 343 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 372 through 373 Processing sheet with id=AA8, first strand: chain 'A' and resid 426 through 429 removed outlier: 3.556A pdb=" N ASP A 471 " --> pdb=" O GLY A 459 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL A 472 " --> pdb=" O MET A 485 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 490 through 495 Processing sheet with id=AB1, first strand: chain 'A' and resid 585 through 588 Processing sheet with id=AB2, first strand: chain 'A' and resid 605 through 606 removed outlier: 3.574A pdb=" N SER A 631 " --> pdb=" O LYS A 606 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 640 through 642 Processing sheet with id=AB4, first strand: chain 'A' and resid 646 through 647 130 hydrogen bonds defined for protein. 315 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: 2.17 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 4753 1.03 - 1.23: 9 1.23 - 1.42: 2250 1.42 - 1.62: 2875 1.62 - 1.81: 37 Bond restraints: 9924 Sorted by residual: bond pdb=" C ILE A 685 " pdb=" O ILE A 685 " ideal model delta sigma weight residual 1.248 1.238 0.010 1.27e-02 6.20e+03 6.13e-01 bond pdb=" N HIS A 182 " pdb=" CA HIS A 182 " ideal model delta sigma weight residual 1.463 1.456 0.008 1.08e-02 8.57e+03 5.19e-01 bond pdb=" N VAL A 469 " pdb=" CA VAL A 469 " ideal model delta sigma weight residual 1.468 1.461 0.007 1.22e-02 6.72e+03 3.27e-01 bond pdb=" C HIS A 182 " pdb=" O HIS A 182 " ideal model delta sigma weight residual 1.244 1.239 0.005 1.00e-02 1.00e+04 2.78e-01 bond pdb=" N ILE A 685 " pdb=" CA ILE A 685 " ideal model delta sigma weight residual 1.467 1.461 0.006 1.09e-02 8.42e+03 2.75e-01 ... (remaining 9919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.78: 16099 0.78 - 1.56: 1536 1.56 - 2.33: 128 2.33 - 3.11: 19 3.11 - 3.89: 16 Bond angle restraints: 17798 Sorted by residual: angle pdb=" N GLU A 598 " pdb=" CA GLU A 598 " pdb=" C GLU A 598 " ideal model delta sigma weight residual 110.44 107.85 2.59 1.20e+00 6.94e-01 4.67e+00 angle pdb=" C LYS A 684 " pdb=" N ILE A 685 " pdb=" CA ILE A 685 " ideal model delta sigma weight residual 119.72 122.93 -3.21 2.01e+00 2.48e-01 2.55e+00 angle pdb=" N SER A 319 " pdb=" CA SER A 319 " pdb=" C SER A 319 " ideal model delta sigma weight residual 108.32 110.91 -2.59 1.64e+00 3.72e-01 2.49e+00 angle pdb=" C MET A 443 " pdb=" N ALA A 444 " pdb=" CA ALA A 444 " ideal model delta sigma weight residual 121.80 124.98 -3.18 2.44e+00 1.68e-01 1.70e+00 angle pdb=" C PHE A 181 " pdb=" CA PHE A 181 " pdb=" CB PHE A 181 " ideal model delta sigma weight residual 113.19 110.11 3.08 2.37e+00 1.78e-01 1.69e+00 ... (remaining 17793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 4539 17.63 - 35.26: 185 35.26 - 52.89: 55 52.89 - 70.52: 21 70.52 - 88.15: 2 Dihedral angle restraints: 4802 sinusoidal: 2600 harmonic: 2202 Sorted by residual: dihedral pdb=" CB CYS A 642 " pdb=" SG CYS A 642 " pdb=" SG CYS A 655 " pdb=" CB CYS A 655 " ideal model delta sinusoidal sigma weight residual 93.00 140.09 -47.09 1 1.00e+01 1.00e-02 3.06e+01 dihedral pdb=" CB CYS A 224 " pdb=" SG CYS A 224 " pdb=" SG CYS A 244 " pdb=" CB CYS A 244 " ideal model delta sinusoidal sigma weight residual 93.00 124.66 -31.66 1 1.00e+01 1.00e-02 1.43e+01 dihedral pdb=" N ARG A 76 " pdb=" CA ARG A 76 " pdb=" CB ARG A 76 " pdb=" CG ARG A 76 " ideal model delta sinusoidal sigma weight residual -180.00 -121.73 -58.27 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 4799 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 421 0.026 - 0.052: 254 0.052 - 0.078: 31 0.078 - 0.104: 42 0.104 - 0.130: 30 Chirality restraints: 778 Sorted by residual: chirality pdb=" CA ILE A 456 " pdb=" N ILE A 456 " pdb=" C ILE A 456 " pdb=" CB ILE A 456 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA ILE A 91 " pdb=" N ILE A 91 " pdb=" C ILE A 91 " pdb=" CB ILE A 91 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" C1 NAG C 2 " pdb=" O4 NAG C 1 " pdb=" C2 NAG C 2 " pdb=" O5 NAG C 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.41 0.01 2.00e-02 2.50e+03 3.92e-01 ... (remaining 775 not shown) Planarity restraints: 1511 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 179 " -0.020 5.00e-02 4.00e+02 3.11e-02 1.55e+00 pdb=" N PRO A 180 " 0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 532 " 0.018 5.00e-02 4.00e+02 2.68e-02 1.15e+00 pdb=" N PRO A 533 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 533 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 533 " 0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 444 " -0.018 5.00e-02 4.00e+02 2.65e-02 1.12e+00 pdb=" N PRO A 445 " 0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 445 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 445 " -0.015 5.00e-02 4.00e+02 ... (remaining 1508 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 666 2.22 - 2.82: 20651 2.82 - 3.41: 23621 3.41 - 4.01: 33712 4.01 - 4.60: 51067 Nonbonded interactions: 129717 Sorted by model distance: nonbonded pdb=" H GLY A 229 " pdb=" O THR A 233 " model vdw 1.629 2.450 nonbonded pdb=" OD1 ASN A 324 " pdb=" H ASP A 325 " model vdw 1.695 2.450 nonbonded pdb=" O GLY A 488 " pdb=" HD1 HIS A 490 " model vdw 1.717 2.450 nonbonded pdb=" HG1 THR A 397 " pdb=" O ARG A 403 " model vdw 1.771 2.450 nonbonded pdb=" OD1 ASN A 450 " pdb=" H ASN A 450 " model vdw 1.774 2.450 ... (remaining 129712 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 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } 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: 3.930 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: 0.070 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.900 Find NCS groups from input model: 0.040 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 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 : 0.003 0.020 5181 Z= 0.117 Angle : 0.464 12.074 7034 Z= 0.239 Chirality : 0.041 0.130 778 Planarity : 0.003 0.031 898 Dihedral : 9.186 81.133 1929 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 0.91 % Allowed : 3.99 % Favored : 95.10 % 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: -0.94 (0.34), residues: 628 helix: -0.67 (1.34), residues: 21 sheet: -0.12 (0.38), residues: 208 loop : -0.90 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 613 TYR 0.008 0.001 TYR A 682 PHE 0.008 0.001 PHE A 529 TRP 0.007 0.001 TRP A 216 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 5170) covalent geometry : angle 0.43347 ( 7007) SS BOND : bond 0.00089 ( 6) SS BOND : angle 0.89451 ( 12) hydrogen bonds : bond 0.23837 ( 130) hydrogen bonds : angle 7.94003 ( 315) link_BETA1-4 : bond 0.00651 ( 2) link_BETA1-4 : angle 5.10018 ( 6) link_NAG-ASN : bond 0.00295 ( 3) link_NAG-ASN : angle 1.79634 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.186 Fit side-chains revert: symmetry clash REVERT: A 97 PHE cc_start: 0.6894 (t80) cc_final: 0.6680 (t80) REVERT: A 320 ILE cc_start: 0.9053 (mt) cc_final: 0.8844 (mt) outliers start: 5 outliers final: 1 residues processed: 73 average time/residue: 0.2675 time to fit residues: 22.8725 Evaluate side-chains 37 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.0170 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN A 695 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.101923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.081994 restraints weight = 20913.673| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 2.45 r_work: 0.2791 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5181 Z= 0.151 Angle : 0.513 8.320 7034 Z= 0.269 Chirality : 0.043 0.152 778 Planarity : 0.003 0.034 898 Dihedral : 5.237 49.263 791 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.09 % Allowed : 6.90 % Favored : 92.01 % 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: -1.11 (0.34), residues: 628 helix: -0.45 (1.44), residues: 21 sheet: -0.24 (0.36), residues: 217 loop : -1.05 (0.31), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.012 0.001 TYR A 491 PHE 0.009 0.001 PHE A 516 TRP 0.008 0.001 TRP A 254 HIS 0.004 0.001 HIS A 676 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 5170) covalent geometry : angle 0.50429 ( 7007) SS BOND : bond 0.00453 ( 6) SS BOND : angle 1.65276 ( 12) hydrogen bonds : bond 0.03891 ( 130) hydrogen bonds : angle 5.54282 ( 315) link_BETA1-4 : bond 0.00361 ( 2) link_BETA1-4 : angle 1.68880 ( 6) link_NAG-ASN : bond 0.00245 ( 3) link_NAG-ASN : angle 1.54620 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.239 Fit side-chains revert: symmetry clash REVERT: A 272 SER cc_start: 0.9129 (t) cc_final: 0.8788 (m) outliers start: 6 outliers final: 5 residues processed: 43 average time/residue: 0.1684 time to fit residues: 9.0193 Evaluate side-chains 43 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 522 GLN Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 601 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 21 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 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 = 0.3200 r_free = 0.3200 target = 0.101867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.081881 restraints weight = 20976.917| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.50 r_work: 0.2787 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2649 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5181 Z= 0.134 Angle : 0.523 11.448 7034 Z= 0.271 Chirality : 0.043 0.164 778 Planarity : 0.003 0.032 898 Dihedral : 5.366 49.040 791 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.09 % Allowed : 7.99 % Favored : 90.93 % 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: -1.15 (0.33), residues: 628 helix: -0.58 (1.39), residues: 21 sheet: -0.27 (0.36), residues: 216 loop : -1.07 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 408 TYR 0.010 0.001 TYR A 491 PHE 0.008 0.001 PHE A 516 TRP 0.007 0.001 TRP A 254 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 5170) covalent geometry : angle 0.50219 ( 7007) SS BOND : bond 0.00496 ( 6) SS BOND : angle 3.23221 ( 12) hydrogen bonds : bond 0.03513 ( 130) hydrogen bonds : angle 5.19447 ( 315) link_BETA1-4 : bond 0.00193 ( 2) link_BETA1-4 : angle 1.63196 ( 6) link_NAG-ASN : bond 0.00201 ( 3) link_NAG-ASN : angle 1.45014 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 41 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.239 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 SER cc_start: 0.9170 (t) cc_final: 0.8845 (m) outliers start: 6 outliers final: 4 residues processed: 39 average time/residue: 0.1953 time to fit residues: 9.3264 Evaluate side-chains 39 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 601 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3187 r_free = 0.3187 target = 0.101054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.081284 restraints weight = 21185.521| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 2.45 r_work: 0.2787 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2650 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5181 Z= 0.154 Angle : 0.504 6.998 7034 Z= 0.262 Chirality : 0.043 0.148 778 Planarity : 0.003 0.034 898 Dihedral : 5.471 47.402 791 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 1.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 1.45 % Allowed : 7.08 % Favored : 91.47 % 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: -1.11 (0.33), residues: 628 helix: 1.41 (1.71), residues: 15 sheet: -0.31 (0.36), residues: 216 loop : -1.09 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 408 TYR 0.012 0.001 TYR A 491 PHE 0.009 0.001 PHE A 529 TRP 0.008 0.001 TRP A 216 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5170) covalent geometry : angle 0.48997 ( 7007) SS BOND : bond 0.00269 ( 6) SS BOND : angle 2.34157 ( 12) hydrogen bonds : bond 0.03198 ( 130) hydrogen bonds : angle 4.95608 ( 315) link_BETA1-4 : bond 0.00180 ( 2) link_BETA1-4 : angle 1.63512 ( 6) link_NAG-ASN : bond 0.00212 ( 3) link_NAG-ASN : angle 1.52129 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 44 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 272 SER cc_start: 0.9158 (t) cc_final: 0.8855 (m) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.1914 time to fit residues: 9.8015 Evaluate side-chains 39 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 601 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 48 optimal weight: 0.9980 chunk 62 optimal weight: 0.4980 chunk 60 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3192 r_free = 0.3192 target = 0.101887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.081997 restraints weight = 20828.111| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 2.44 r_work: 0.2762 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2625 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5181 Z= 0.139 Angle : 0.478 6.120 7034 Z= 0.250 Chirality : 0.043 0.145 778 Planarity : 0.003 0.032 898 Dihedral : 5.494 47.323 791 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.09 % Allowed : 7.99 % Favored : 90.93 % 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: -1.08 (0.33), residues: 628 helix: 1.36 (1.70), residues: 15 sheet: -0.25 (0.36), residues: 216 loop : -1.09 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.010 0.001 TYR A 491 PHE 0.008 0.001 PHE A 516 TRP 0.006 0.001 TRP A 216 HIS 0.003 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 5170) covalent geometry : angle 0.46982 ( 7007) SS BOND : bond 0.00321 ( 6) SS BOND : angle 1.54314 ( 12) hydrogen bonds : bond 0.03019 ( 130) hydrogen bonds : angle 4.84380 ( 315) link_BETA1-4 : bond 0.00182 ( 2) link_BETA1-4 : angle 1.58274 ( 6) link_NAG-ASN : bond 0.00188 ( 3) link_NAG-ASN : angle 1.43250 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 42 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.178 Fit side-chains revert: symmetry clash REVERT: A 272 SER cc_start: 0.9160 (t) cc_final: 0.8848 (m) REVERT: A 519 ASP cc_start: 0.7899 (m-30) cc_final: 0.7642 (t0) outliers start: 6 outliers final: 5 residues processed: 40 average time/residue: 0.2159 time to fit residues: 10.4498 Evaluate side-chains 39 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 601 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 51 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3213 r_free = 0.3213 target = 0.102418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.082359 restraints weight = 21170.656| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 2.47 r_work: 0.2792 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5181 Z= 0.141 Angle : 0.475 5.773 7034 Z= 0.249 Chirality : 0.043 0.146 778 Planarity : 0.003 0.032 898 Dihedral : 5.514 47.155 791 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.63 % Allowed : 7.80 % Favored : 90.56 % 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: -1.09 (0.33), residues: 628 helix: 1.30 (1.67), residues: 15 sheet: -0.24 (0.36), residues: 216 loop : -1.10 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 166 TYR 0.011 0.001 TYR A 491 PHE 0.008 0.001 PHE A 516 TRP 0.007 0.001 TRP A 216 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 5170) covalent geometry : angle 0.46739 ( 7007) SS BOND : bond 0.00291 ( 6) SS BOND : angle 1.42699 ( 12) hydrogen bonds : bond 0.02949 ( 130) hydrogen bonds : angle 4.78470 ( 315) link_BETA1-4 : bond 0.00192 ( 2) link_BETA1-4 : angle 1.57556 ( 6) link_NAG-ASN : bond 0.00205 ( 3) link_NAG-ASN : angle 1.45873 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 46 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 37 time to evaluate : 0.203 Fit side-chains revert: symmetry clash REVERT: A 272 SER cc_start: 0.9162 (t) cc_final: 0.8864 (m) REVERT: A 519 ASP cc_start: 0.7930 (m-30) cc_final: 0.7626 (t0) outliers start: 9 outliers final: 7 residues processed: 44 average time/residue: 0.1781 time to fit residues: 9.6827 Evaluate side-chains 43 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 601 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 42 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 61 optimal weight: 0.0470 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5878 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.103340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.083071 restraints weight = 21141.263| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 2.49 r_work: 0.2813 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2674 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 5181 Z= 0.103 Angle : 0.451 5.457 7034 Z= 0.236 Chirality : 0.042 0.145 778 Planarity : 0.003 0.030 898 Dihedral : 5.425 47.141 791 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 1.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.45 % Allowed : 8.71 % Favored : 89.84 % 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: -1.03 (0.33), residues: 628 helix: 1.16 (1.61), residues: 15 sheet: -0.20 (0.36), residues: 216 loop : -1.05 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 408 TYR 0.009 0.001 TYR A 491 PHE 0.007 0.001 PHE A 516 TRP 0.005 0.001 TRP A 254 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 5170) covalent geometry : angle 0.44439 ( 7007) SS BOND : bond 0.00277 ( 6) SS BOND : angle 1.24259 ( 12) hydrogen bonds : bond 0.02706 ( 130) hydrogen bonds : angle 4.67224 ( 315) link_BETA1-4 : bond 0.00226 ( 2) link_BETA1-4 : angle 1.51301 ( 6) link_NAG-ASN : bond 0.00194 ( 3) link_NAG-ASN : angle 1.36069 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.253 Fit side-chains revert: symmetry clash REVERT: A 272 SER cc_start: 0.9156 (t) cc_final: 0.8858 (m) REVERT: A 519 ASP cc_start: 0.7927 (m-30) cc_final: 0.7720 (t0) outliers start: 8 outliers final: 8 residues processed: 43 average time/residue: 0.1904 time to fit residues: 10.1441 Evaluate side-chains 44 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 192 GLN Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 601 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.102549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.082305 restraints weight = 21124.771| |-----------------------------------------------------------------------------| r_work (start): 0.2905 rms_B_bonded: 2.48 r_work: 0.2804 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5181 Z= 0.137 Angle : 0.469 5.603 7034 Z= 0.245 Chirality : 0.042 0.146 778 Planarity : 0.003 0.031 898 Dihedral : 5.483 46.869 791 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.45 % Allowed : 8.71 % Favored : 89.84 % 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: -1.09 (0.33), residues: 628 helix: 1.26 (1.63), residues: 15 sheet: -0.24 (0.36), residues: 216 loop : -1.10 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.011 0.001 TYR A 491 PHE 0.008 0.001 PHE A 516 TRP 0.006 0.001 TRP A 216 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5170) covalent geometry : angle 0.46151 ( 7007) SS BOND : bond 0.00283 ( 6) SS BOND : angle 1.26346 ( 12) hydrogen bonds : bond 0.02897 ( 130) hydrogen bonds : angle 4.70894 ( 315) link_BETA1-4 : bond 0.00171 ( 2) link_BETA1-4 : angle 1.55356 ( 6) link_NAG-ASN : bond 0.00214 ( 3) link_NAG-ASN : angle 1.45450 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 45 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.260 Fit side-chains revert: symmetry clash REVERT: A 272 SER cc_start: 0.9170 (t) cc_final: 0.8866 (m) REVERT: A 519 ASP cc_start: 0.7957 (m-30) cc_final: 0.7742 (t0) outliers start: 8 outliers final: 7 residues processed: 43 average time/residue: 0.1806 time to fit residues: 9.5384 Evaluate side-chains 44 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 601 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 58 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3216 r_free = 0.3216 target = 0.102592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.082309 restraints weight = 21116.157| |-----------------------------------------------------------------------------| r_work (start): 0.2895 rms_B_bonded: 2.48 r_work: 0.2792 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2653 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5181 Z= 0.137 Angle : 0.470 5.568 7034 Z= 0.246 Chirality : 0.043 0.144 778 Planarity : 0.003 0.031 898 Dihedral : 5.505 46.825 791 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.45 % Allowed : 9.07 % Favored : 89.47 % 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: -1.08 (0.33), residues: 628 helix: 1.21 (1.62), residues: 15 sheet: -0.23 (0.36), residues: 216 loop : -1.09 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.010 0.001 TYR A 491 PHE 0.008 0.001 PHE A 516 TRP 0.006 0.001 TRP A 216 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 5170) covalent geometry : angle 0.46285 ( 7007) SS BOND : bond 0.00282 ( 6) SS BOND : angle 1.23774 ( 12) hydrogen bonds : bond 0.02859 ( 130) hydrogen bonds : angle 4.69453 ( 315) link_BETA1-4 : bond 0.00184 ( 2) link_BETA1-4 : angle 1.55319 ( 6) link_NAG-ASN : bond 0.00188 ( 3) link_NAG-ASN : angle 1.41208 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 44 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.220 Fit side-chains revert: symmetry clash REVERT: A 272 SER cc_start: 0.9168 (t) cc_final: 0.8868 (m) REVERT: A 519 ASP cc_start: 0.7966 (m-30) cc_final: 0.7743 (t0) outliers start: 8 outliers final: 7 residues processed: 42 average time/residue: 0.1524 time to fit residues: 8.0351 Evaluate side-chains 42 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 601 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 41 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 0.4980 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 = 0.3230 r_free = 0.3230 target = 0.103556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.083606 restraints weight = 20924.060| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 2.44 r_work: 0.2812 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5181 Z= 0.094 Angle : 0.445 5.145 7034 Z= 0.233 Chirality : 0.042 0.143 778 Planarity : 0.003 0.029 898 Dihedral : 5.373 46.858 791 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.27 % Allowed : 9.26 % Favored : 89.47 % 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: -1.01 (0.33), residues: 628 helix: 1.13 (1.59), residues: 15 sheet: -0.18 (0.36), residues: 216 loop : -1.04 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 408 TYR 0.009 0.001 TYR A 491 PHE 0.007 0.001 PHE A 516 TRP 0.005 0.001 TRP A 254 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 5170) covalent geometry : angle 0.43867 ( 7007) SS BOND : bond 0.00261 ( 6) SS BOND : angle 1.07927 ( 12) hydrogen bonds : bond 0.02552 ( 130) hydrogen bonds : angle 4.55482 ( 315) link_BETA1-4 : bond 0.00239 ( 2) link_BETA1-4 : angle 1.47521 ( 6) link_NAG-ASN : bond 0.00198 ( 3) link_NAG-ASN : angle 1.30856 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1256 Ramachandran restraints generated. 628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 43 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.170 Fit side-chains revert: symmetry clash REVERT: A 272 SER cc_start: 0.9159 (t) cc_final: 0.8873 (m) outliers start: 7 outliers final: 7 residues processed: 41 average time/residue: 0.1897 time to fit residues: 9.6236 Evaluate side-chains 43 residues out of total 553 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 299 ASP Chi-restraints excluded: chain A residue 548 MET Chi-restraints excluded: chain A residue 556 THR Chi-restraints excluded: chain A residue 601 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 47 optimal weight: 0.4980 chunk 44 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3221 r_free = 0.3221 target = 0.102926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.082957 restraints weight = 21108.705| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 2.45 r_work: 0.2802 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2661 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5181 Z= 0.126 Angle : 0.462 5.345 7034 Z= 0.242 Chirality : 0.042 0.144 778 Planarity : 0.003 0.029 898 Dihedral : 5.427 46.615 791 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 1.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.63 % Allowed : 9.07 % Favored : 89.29 % 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: -1.03 (0.33), residues: 628 helix: 1.25 (1.61), residues: 15 sheet: -0.19 (0.36), residues: 216 loop : -1.06 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 166 TYR 0.009 0.001 TYR A 491 PHE 0.008 0.001 PHE A 516 TRP 0.006 0.001 TRP A 216 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5170) covalent geometry : angle 0.45526 ( 7007) SS BOND : bond 0.00269 ( 6) SS BOND : angle 1.15983 ( 12) hydrogen bonds : bond 0.02731 ( 130) hydrogen bonds : angle 4.61028 ( 315) link_BETA1-4 : bond 0.00212 ( 2) link_BETA1-4 : angle 1.49980 ( 6) link_NAG-ASN : bond 0.00207 ( 3) link_NAG-ASN : angle 1.38122 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.91 seconds wall clock time: 37 minutes 22.14 seconds (2242.14 seconds total)