Starting phenix.real_space_refine on Wed Feb 4 09:46:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i0n_52562/02_2026/9i0n_52562_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i0n_52562/02_2026/9i0n_52562.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9i0n_52562/02_2026/9i0n_52562.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i0n_52562/02_2026/9i0n_52562.map" model { file = "/net/cci-nas-00/data/ceres_data/9i0n_52562/02_2026/9i0n_52562_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i0n_52562/02_2026/9i0n_52562_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.061 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 3111 2.51 5 N 825 2.21 5 O 977 1.98 5 H 4643 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: 9581 Number of models: 1 Model: "" Number of chains: 4 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: 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: "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: "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: 1.73, per 1000 atoms: 0.18 Number of scatterers: 9581 At special positions: 0 Unit cell: (63.58, 93.5, 92.752, 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 977 8.00 N 825 7.00 C 3111 6.00 H 4643 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=2.04 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 B 1 " - " NAG B 2 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG A 801 " - " ASN A 129 " " NAG B 1 " - " ASN A 373 " " NAG C 1 " - " ASN A 549 " Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 250.3 milliseconds 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1132 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 12 sheets defined 3.4% alpha, 29.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 58 through 65 removed outlier: 3.602A pdb=" N LYS A 62 " --> pdb=" O ASP A 58 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ASN A 65 " --> pdb=" O ALA A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 437 Processing helix chain 'A' and resid 580 through 582 No H-bonds generated for 'chain 'A' and resid 580 through 582' 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 71 removed outlier: 3.704A pdb=" N THR A 556 " --> pdb=" O GLN A 563 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N SER A 551 " --> pdb=" O LEU A 539 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N LEU A 539 " --> pdb=" O SER A 551 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP A 553 " --> pdb=" O THR A 537 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 80 through 84 removed outlier: 4.413A pdb=" N VAL A 90 " --> pdb=" O VAL A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 152 Processing sheet with id=AA4, first strand: chain 'A' and resid 188 through 189 removed outlier: 6.845A 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: 3.964A pdb=" N LEU A 225 " --> pdb=" O THR A 237 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N LEU A 251 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N VAL A 268 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU A 253 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS A 269 " --> pdb=" O MET A 285 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N SER A 283 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N PHE A 273 " --> pdb=" O PHE A 281 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N PHE A 281 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N LEU A 275 " --> pdb=" O PHE A 279 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N PHE A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 318 through 323 removed outlier: 7.034A pdb=" N TYR A 318 " --> pdb=" O ASP A 333 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ASP A 333 " --> pdb=" O TYR A 318 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ILE A 320 " --> pdb=" O HIS A 331 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N HIS A 331 " --> pdb=" O ILE A 320 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA A 322 " --> pdb=" O PHE A 329 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N VAL A 328 " --> pdb=" O SER A 346 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY A 341 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 5.244A pdb=" N ASP A 358 " --> pdb=" O GLY A 341 " (cutoff:3.500A) removed outlier: 6.470A 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: 3.531A pdb=" N SER A 426 " --> pdb=" O GLY A 462 " (cutoff:3.500A) removed outlier: 6.908A 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 584 through 588 removed outlier: 3.613A pdb=" N GLN A 608 " --> pdb=" O GLN A 629 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 640 through 642 Processing sheet with id=AB3, first strand: chain 'A' and resid 646 through 647 127 hydrogen bonds defined for protein. 312 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4642 1.04 - 1.23: 106 1.23 - 1.43: 2106 1.43 - 1.62: 2805 1.62 - 1.82: 37 Bond restraints: 9696 Sorted by residual: bond pdb=" C ALA A 222 " pdb=" N VAL A 223 " ideal model delta sigma weight residual 1.334 1.323 0.011 1.29e-02 6.01e+03 6.67e-01 bond pdb=" CA VAL A 374 " pdb=" CB VAL A 374 " ideal model delta sigma weight residual 1.540 1.530 0.010 1.36e-02 5.41e+03 5.22e-01 bond pdb=" CA VAL A 469 " pdb=" CB VAL A 469 " ideal model delta sigma weight residual 1.539 1.530 0.009 1.58e-02 4.01e+03 3.33e-01 bond pdb=" C ALA A 323 " pdb=" N ASN A 324 " ideal model delta sigma weight residual 1.332 1.324 0.008 1.40e-02 5.10e+03 3.20e-01 bond pdb=" C VAL A 374 " pdb=" O VAL A 374 " ideal model delta sigma weight residual 1.236 1.230 0.006 1.19e-02 7.06e+03 2.80e-01 ... (remaining 9691 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 16745 1.15 - 2.31: 610 2.31 - 3.46: 26 3.46 - 4.61: 4 4.61 - 5.76: 1 Bond angle restraints: 17386 Sorted by residual: angle pdb=" CA CYS A 601 " pdb=" CB CYS A 601 " pdb=" SG CYS A 601 " ideal model delta sigma weight residual 114.40 118.42 -4.02 2.30e+00 1.89e-01 3.05e+00 angle pdb=" CA LEU A 198 " pdb=" CB LEU A 198 " pdb=" CG LEU A 198 " ideal model delta sigma weight residual 116.30 122.06 -5.76 3.50e+00 8.16e-02 2.71e+00 angle pdb=" N VAL A 374 " pdb=" CA VAL A 374 " pdb=" C VAL A 374 " ideal model delta sigma weight residual 109.34 106.77 2.57 2.08e+00 2.31e-01 1.52e+00 angle pdb=" N LYS A 221 " pdb=" CA LYS A 221 " pdb=" C LYS A 221 " ideal model delta sigma weight residual 113.61 115.42 -1.81 1.50e+00 4.44e-01 1.46e+00 angle pdb=" N ASP A 116 " pdb=" CA ASP A 116 " pdb=" CB ASP A 116 " ideal model delta sigma weight residual 111.54 109.81 1.73 1.45e+00 4.76e-01 1.43e+00 ... (remaining 17381 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 4405 16.50 - 33.00: 194 33.00 - 49.49: 58 49.49 - 65.99: 32 65.99 - 82.49: 4 Dihedral angle restraints: 4693 sinusoidal: 2538 harmonic: 2155 Sorted by residual: dihedral pdb=" N LYS A 654 " pdb=" CA LYS A 654 " pdb=" CB LYS A 654 " pdb=" CG LYS A 654 " ideal model delta sinusoidal sigma weight residual -180.00 -123.95 -56.05 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" CA GLN A 314 " pdb=" CB GLN A 314 " pdb=" CG GLN A 314 " pdb=" CD GLN A 314 " ideal model delta sinusoidal sigma weight residual 180.00 124.11 55.89 3 1.50e+01 4.44e-03 9.37e+00 dihedral pdb=" CB ARG A 546 " pdb=" CG ARG A 546 " pdb=" CD ARG A 546 " pdb=" NE ARG A 546 " ideal model delta sinusoidal sigma weight residual -60.00 -114.60 54.60 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 4690 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 441 0.029 - 0.057: 220 0.057 - 0.086: 32 0.086 - 0.115: 46 0.115 - 0.143: 21 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA ILE A 501 " pdb=" N ILE A 501 " pdb=" C ILE A 501 " pdb=" CB ILE A 501 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ILE A 602 " pdb=" N ILE A 602 " pdb=" C ILE A 602 " pdb=" CB ILE A 602 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-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 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 757 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 629 " -0.019 5.00e-02 4.00e+02 2.95e-02 1.39e+00 pdb=" N PRO A 630 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 630 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 630 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 179 " -0.019 5.00e-02 4.00e+02 2.93e-02 1.38e+00 pdb=" N PRO A 180 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 180 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 180 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 448 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO A 449 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 449 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 449 " 0.016 5.00e-02 4.00e+02 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.21: 582 2.21 - 2.81: 19402 2.81 - 3.41: 23104 3.41 - 4.00: 32905 4.00 - 4.60: 49963 Nonbonded interactions: 125956 Sorted by model distance: nonbonded pdb=" O SER A 243 " pdb=" H ASP A 247 " model vdw 1.615 2.450 nonbonded pdb=" HG1 THR A 397 " pdb=" O ARG A 403 " model vdw 1.628 2.450 nonbonded pdb="HH11 ARG A 113 " pdb=" OE2 GLU A 115 " model vdw 1.708 2.450 nonbonded pdb=" OE1 GLU A 411 " pdb=" H GLU A 411 " model vdw 1.710 2.450 nonbonded pdb="HE22 GLN A 316 " pdb=" O ASP A 333 " model vdw 1.717 2.450 ... (remaining 125951 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 'B' selection = chain 'C' } 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: 4.090 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: 0.060 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.860 Find NCS groups from input model: 0.040 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 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 0.021 5064 Z= 0.119 Angle : 0.444 5.763 6877 Z= 0.231 Chirality : 0.043 0.143 760 Planarity : 0.003 0.029 878 Dihedral : 9.759 82.491 1884 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 0.93 % Allowed : 2.42 % Favored : 96.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.33), residues: 615 helix: -2.28 (1.02), residues: 25 sheet: 0.61 (0.37), residues: 202 loop : -0.66 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 57 TYR 0.009 0.001 TYR A 491 PHE 0.009 0.001 PHE A 329 TRP 0.008 0.001 TRP A 254 HIS 0.002 0.001 HIS A 590 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 5053) covalent geometry : angle 0.43421 ( 6850) SS BOND : bond 0.00234 ( 6) SS BOND : angle 0.94753 ( 12) hydrogen bonds : bond 0.23380 ( 127) hydrogen bonds : angle 7.96919 ( 312) link_BETA1-4 : bond 0.00420 ( 2) link_BETA1-4 : angle 1.70549 ( 6) link_NAG-ASN : bond 0.00309 ( 3) link_NAG-ASN : angle 1.99833 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.222 Fit side-chains REVERT: A 247 ASP cc_start: 0.7230 (t0) cc_final: 0.6999 (m-30) REVERT: A 546 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8271 (ttm110) REVERT: A 582 LYS cc_start: 0.8149 (tttm) cc_final: 0.7901 (tptp) REVERT: A 623 ASP cc_start: 0.7902 (t0) cc_final: 0.7644 (t0) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.2068 time to fit residues: 15.2782 Evaluate side-chains 50 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 688 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 54 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 186 GLN A 211 ASN A 316 GLN A 412 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.130758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.100381 restraints weight = 17025.552| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.60 r_work: 0.2819 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.0852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 5064 Z= 0.111 Angle : 0.490 7.954 6877 Z= 0.264 Chirality : 0.044 0.152 760 Planarity : 0.003 0.031 878 Dihedral : 5.141 52.883 784 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.93 % Allowed : 5.21 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.33), residues: 615 helix: -2.05 (1.08), residues: 26 sheet: 0.63 (0.36), residues: 203 loop : -0.68 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 160 TYR 0.013 0.001 TYR A 189 PHE 0.012 0.001 PHE A 329 TRP 0.008 0.001 TRP A 254 HIS 0.002 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 5053) covalent geometry : angle 0.48418 ( 6850) SS BOND : bond 0.00281 ( 6) SS BOND : angle 0.80100 ( 12) hydrogen bonds : bond 0.04020 ( 127) hydrogen bonds : angle 5.55021 ( 312) link_BETA1-4 : bond 0.00252 ( 2) link_BETA1-4 : angle 1.50367 ( 6) link_NAG-ASN : bond 0.00300 ( 3) link_NAG-ASN : angle 1.63801 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.226 Fit side-chains REVERT: A 198 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8361 (pp) REVERT: A 211 ASN cc_start: 0.8501 (t0) cc_final: 0.8279 (t0) REVERT: A 247 ASP cc_start: 0.7313 (t0) cc_final: 0.6983 (m-30) REVERT: A 546 ARG cc_start: 0.8783 (OUTLIER) cc_final: 0.8334 (ttm110) REVERT: A 582 LYS cc_start: 0.8179 (tttm) cc_final: 0.7746 (tptp) REVERT: A 623 ASP cc_start: 0.7938 (t0) cc_final: 0.7675 (t0) outliers start: 5 outliers final: 2 residues processed: 55 average time/residue: 0.1670 time to fit residues: 11.3797 Evaluate side-chains 50 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 688 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 0.0970 chunk 24 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.138298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.110774 restraints weight = 16722.152| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.28 r_work: 0.3090 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2945 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5064 Z= 0.121 Angle : 0.476 6.900 6877 Z= 0.253 Chirality : 0.044 0.151 760 Planarity : 0.003 0.035 878 Dihedral : 5.116 52.875 782 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.49 % Allowed : 7.08 % Favored : 91.43 % 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: -0.48 (0.33), residues: 615 helix: -2.09 (1.07), residues: 26 sheet: 0.69 (0.37), residues: 203 loop : -0.77 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 160 TYR 0.011 0.001 TYR A 189 PHE 0.010 0.001 PHE A 236 TRP 0.009 0.001 TRP A 254 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5053) covalent geometry : angle 0.46853 ( 6850) SS BOND : bond 0.00337 ( 6) SS BOND : angle 1.25020 ( 12) hydrogen bonds : bond 0.03809 ( 127) hydrogen bonds : angle 5.30354 ( 312) link_BETA1-4 : bond 0.00294 ( 2) link_BETA1-4 : angle 1.51677 ( 6) link_NAG-ASN : bond 0.00273 ( 3) link_NAG-ASN : angle 1.54892 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.191 Fit side-chains REVERT: A 108 GLN cc_start: 0.6157 (OUTLIER) cc_final: 0.5845 (pp30) REVERT: A 198 LEU cc_start: 0.8882 (OUTLIER) cc_final: 0.8483 (pp) REVERT: A 211 ASN cc_start: 0.8459 (t0) cc_final: 0.8253 (t0) REVERT: A 546 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8377 (ttm110) REVERT: A 582 LYS cc_start: 0.8216 (tttm) cc_final: 0.7865 (tptp) REVERT: A 623 ASP cc_start: 0.7908 (t0) cc_final: 0.7644 (t0) outliers start: 8 outliers final: 3 residues processed: 52 average time/residue: 0.1883 time to fit residues: 11.9515 Evaluate side-chains 50 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 688 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 60 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 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 = 0.3545 r_free = 0.3545 target = 0.132578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.103334 restraints weight = 17143.648| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 2.48 r_work: 0.2921 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5064 Z= 0.132 Angle : 0.482 7.278 6877 Z= 0.256 Chirality : 0.044 0.153 760 Planarity : 0.003 0.035 878 Dihedral : 5.152 52.676 782 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.86 % Allowed : 7.08 % Favored : 91.06 % 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: -0.38 (0.33), residues: 615 helix: -1.10 (1.32), residues: 20 sheet: 0.67 (0.36), residues: 203 loop : -0.72 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 403 TYR 0.011 0.001 TYR A 189 PHE 0.011 0.001 PHE A 236 TRP 0.009 0.001 TRP A 254 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 5053) covalent geometry : angle 0.47423 ( 6850) SS BOND : bond 0.00329 ( 6) SS BOND : angle 1.36837 ( 12) hydrogen bonds : bond 0.03450 ( 127) hydrogen bonds : angle 5.17549 ( 312) link_BETA1-4 : bond 0.00267 ( 2) link_BETA1-4 : angle 1.53868 ( 6) link_NAG-ASN : bond 0.00278 ( 3) link_NAG-ASN : angle 1.55015 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 56 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.194 Fit side-chains REVERT: A 108 GLN cc_start: 0.5979 (OUTLIER) cc_final: 0.5629 (pp30) REVERT: A 169 ASP cc_start: 0.7878 (m-30) cc_final: 0.7516 (m-30) REVERT: A 198 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8365 (pp) REVERT: A 211 ASN cc_start: 0.8413 (t0) cc_final: 0.8172 (t0) REVERT: A 546 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8308 (ttm110) REVERT: A 582 LYS cc_start: 0.8182 (tttm) cc_final: 0.7776 (tptp) REVERT: A 623 ASP cc_start: 0.7930 (t0) cc_final: 0.7663 (t0) outliers start: 10 outliers final: 4 residues processed: 52 average time/residue: 0.2063 time to fit residues: 12.9550 Evaluate side-chains 52 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 688 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 0 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 3 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- 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 = 0.3434 r_free = 0.3434 target = 0.126414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.095001 restraints weight = 17300.175| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 2.71 r_work: 0.2802 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5064 Z= 0.119 Angle : 0.479 6.929 6877 Z= 0.253 Chirality : 0.044 0.149 760 Planarity : 0.003 0.037 878 Dihedral : 5.139 52.411 782 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 0.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.68 % Allowed : 7.82 % Favored : 90.50 % 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: -0.36 (0.33), residues: 615 helix: -1.14 (1.32), residues: 20 sheet: 0.70 (0.36), residues: 203 loop : -0.72 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.010 0.001 TYR A 189 PHE 0.010 0.001 PHE A 236 TRP 0.008 0.001 TRP A 254 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 5053) covalent geometry : angle 0.46364 ( 6850) SS BOND : bond 0.00172 ( 6) SS BOND : angle 2.43215 ( 12) hydrogen bonds : bond 0.03291 ( 127) hydrogen bonds : angle 5.12188 ( 312) link_BETA1-4 : bond 0.00275 ( 2) link_BETA1-4 : angle 1.49145 ( 6) link_NAG-ASN : bond 0.00240 ( 3) link_NAG-ASN : angle 1.47566 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.205 Fit side-chains REVERT: A 108 GLN cc_start: 0.5890 (OUTLIER) cc_final: 0.5539 (pp30) REVERT: A 169 ASP cc_start: 0.7874 (m-30) cc_final: 0.7520 (m-30) REVERT: A 198 LEU cc_start: 0.8741 (OUTLIER) cc_final: 0.8352 (pp) REVERT: A 211 ASN cc_start: 0.8417 (t0) cc_final: 0.8162 (t0) REVERT: A 306 MET cc_start: 0.8238 (ttp) cc_final: 0.7988 (ttm) REVERT: A 546 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.8301 (ttm110) REVERT: A 582 LYS cc_start: 0.8227 (tttm) cc_final: 0.7783 (tptp) REVERT: A 623 ASP cc_start: 0.7963 (t0) cc_final: 0.7473 (t0) outliers start: 9 outliers final: 4 residues processed: 50 average time/residue: 0.2335 time to fit residues: 13.7570 Evaluate side-chains 51 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 688 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 58 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 0.0000 chunk 48 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.133112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.103847 restraints weight = 17006.930| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.47 r_work: 0.2852 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5064 Z= 0.118 Angle : 0.480 6.942 6877 Z= 0.254 Chirality : 0.044 0.148 760 Planarity : 0.003 0.037 878 Dihedral : 5.127 52.208 782 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.12 % Allowed : 9.12 % Favored : 89.76 % 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: -0.34 (0.33), residues: 615 helix: -1.13 (1.30), residues: 20 sheet: 0.73 (0.36), residues: 203 loop : -0.71 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.009 0.001 TYR A 189 PHE 0.011 0.001 PHE A 236 TRP 0.008 0.001 TRP A 254 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 5053) covalent geometry : angle 0.46341 ( 6850) SS BOND : bond 0.00170 ( 6) SS BOND : angle 2.61726 ( 12) hydrogen bonds : bond 0.03181 ( 127) hydrogen bonds : angle 5.06547 ( 312) link_BETA1-4 : bond 0.00348 ( 2) link_BETA1-4 : angle 1.48402 ( 6) link_NAG-ASN : bond 0.00263 ( 3) link_NAG-ASN : angle 1.47681 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 50 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.240 Fit side-chains REVERT: A 108 GLN cc_start: 0.5916 (OUTLIER) cc_final: 0.5561 (pp30) REVERT: A 169 ASP cc_start: 0.7814 (m-30) cc_final: 0.7457 (m-30) REVERT: A 198 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8325 (pp) REVERT: A 211 ASN cc_start: 0.8356 (t0) cc_final: 0.8089 (t0) REVERT: A 306 MET cc_start: 0.8193 (ttp) cc_final: 0.7950 (ttm) REVERT: A 582 LYS cc_start: 0.8205 (tttm) cc_final: 0.7776 (tptp) REVERT: A 623 ASP cc_start: 0.7896 (t0) cc_final: 0.7416 (t0) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.1896 time to fit residues: 10.6282 Evaluate side-chains 50 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 688 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 53 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 38 optimal weight: 0.0770 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.135982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.108132 restraints weight = 16963.503| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.31 r_work: 0.3046 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5064 Z= 0.103 Angle : 0.457 6.614 6877 Z= 0.242 Chirality : 0.044 0.145 760 Planarity : 0.003 0.036 878 Dihedral : 4.654 51.669 778 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.49 % Allowed : 8.94 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.33), residues: 615 helix: -1.09 (1.31), residues: 20 sheet: 0.78 (0.36), residues: 203 loop : -0.70 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.009 0.001 TYR A 189 PHE 0.010 0.001 PHE A 236 TRP 0.007 0.001 TRP A 228 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 5053) covalent geometry : angle 0.44590 ( 6850) SS BOND : bond 0.00205 ( 6) SS BOND : angle 1.96737 ( 12) hydrogen bonds : bond 0.03006 ( 127) hydrogen bonds : angle 4.98437 ( 312) link_BETA1-4 : bond 0.00302 ( 2) link_BETA1-4 : angle 1.41582 ( 6) link_NAG-ASN : bond 0.00258 ( 3) link_NAG-ASN : angle 1.38864 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 55 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.208 Fit side-chains REVERT: A 108 GLN cc_start: 0.6055 (OUTLIER) cc_final: 0.5721 (pp30) REVERT: A 169 ASP cc_start: 0.7822 (m-30) cc_final: 0.7457 (m-30) REVERT: A 198 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8371 (pp) REVERT: A 211 ASN cc_start: 0.8405 (t0) cc_final: 0.8163 (t0) REVERT: A 306 MET cc_start: 0.8175 (ttp) cc_final: 0.7963 (ttm) REVERT: A 546 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.8255 (ttm110) REVERT: A 582 LYS cc_start: 0.8228 (tttm) cc_final: 0.7846 (tptp) REVERT: A 623 ASP cc_start: 0.7900 (t0) cc_final: 0.7423 (t0) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.2090 time to fit residues: 12.7971 Evaluate side-chains 52 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 688 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 50 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3546 r_free = 0.3546 target = 0.132705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.103426 restraints weight = 17033.402| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.47 r_work: 0.3015 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5064 Z= 0.129 Angle : 0.478 7.028 6877 Z= 0.252 Chirality : 0.044 0.150 760 Planarity : 0.003 0.037 878 Dihedral : 4.748 51.393 778 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.49 % Allowed : 9.87 % Favored : 88.64 % 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: -0.32 (0.33), residues: 615 helix: -1.06 (1.30), residues: 20 sheet: 0.77 (0.36), residues: 203 loop : -0.72 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.009 0.001 TYR A 239 PHE 0.011 0.001 PHE A 236 TRP 0.008 0.001 TRP A 254 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5053) covalent geometry : angle 0.46474 ( 6850) SS BOND : bond 0.00213 ( 6) SS BOND : angle 2.20834 ( 12) hydrogen bonds : bond 0.03169 ( 127) hydrogen bonds : angle 5.04435 ( 312) link_BETA1-4 : bond 0.00300 ( 2) link_BETA1-4 : angle 1.44676 ( 6) link_NAG-ASN : bond 0.00264 ( 3) link_NAG-ASN : angle 1.47476 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.259 Fit side-chains REVERT: A 108 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.5775 (pp30) REVERT: A 169 ASP cc_start: 0.7923 (m-30) cc_final: 0.7552 (m-30) REVERT: A 198 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8444 (pp) REVERT: A 211 ASN cc_start: 0.8465 (t0) cc_final: 0.8214 (t0) REVERT: A 546 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8268 (ttm110) REVERT: A 582 LYS cc_start: 0.8232 (tttm) cc_final: 0.7861 (tptp) REVERT: A 623 ASP cc_start: 0.7886 (t0) cc_final: 0.7401 (t0) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.2234 time to fit residues: 12.7929 Evaluate side-chains 51 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 43 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 688 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 10 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.130141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.100645 restraints weight = 17182.789| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.47 r_work: 0.3009 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5064 Z= 0.128 Angle : 0.477 7.065 6877 Z= 0.252 Chirality : 0.044 0.151 760 Planarity : 0.003 0.037 878 Dihedral : 4.769 51.142 778 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 0.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 1.68 % Allowed : 9.68 % Favored : 88.64 % 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: -0.34 (0.33), residues: 615 helix: -1.10 (1.29), residues: 20 sheet: 0.77 (0.36), residues: 203 loop : -0.74 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 403 TYR 0.009 0.001 TYR A 189 PHE 0.011 0.001 PHE A 236 TRP 0.008 0.001 TRP A 254 HIS 0.003 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 5053) covalent geometry : angle 0.46532 ( 6850) SS BOND : bond 0.00220 ( 6) SS BOND : angle 1.97900 ( 12) hydrogen bonds : bond 0.03117 ( 127) hydrogen bonds : angle 5.02541 ( 312) link_BETA1-4 : bond 0.00309 ( 2) link_BETA1-4 : angle 1.47149 ( 6) link_NAG-ASN : bond 0.00263 ( 3) link_NAG-ASN : angle 1.47123 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 52 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.259 Fit side-chains REVERT: A 108 GLN cc_start: 0.6166 (OUTLIER) cc_final: 0.5779 (pp30) REVERT: A 169 ASP cc_start: 0.7959 (m-30) cc_final: 0.7611 (m-30) REVERT: A 198 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8448 (pp) REVERT: A 211 ASN cc_start: 0.8474 (t0) cc_final: 0.8235 (t0) REVERT: A 306 MET cc_start: 0.7943 (ttm) cc_final: 0.7594 (ttp) REVERT: A 520 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.8026 (tt0) REVERT: A 546 ARG cc_start: 0.8798 (OUTLIER) cc_final: 0.8241 (ttm110) REVERT: A 582 LYS cc_start: 0.8235 (tttm) cc_final: 0.7875 (tptp) REVERT: A 623 ASP cc_start: 0.7884 (t0) cc_final: 0.7395 (t0) outliers start: 9 outliers final: 5 residues processed: 48 average time/residue: 0.2232 time to fit residues: 12.9029 Evaluate side-chains 53 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 198 LEU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 520 GLU Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 688 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 51 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 54 optimal weight: 0.0980 chunk 57 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 46 optimal weight: 0.4980 chunk 41 optimal weight: 0.2980 chunk 52 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.133545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.104342 restraints weight = 17013.583| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.46 r_work: 0.2983 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 5064 Z= 0.091 Angle : 0.447 6.463 6877 Z= 0.237 Chirality : 0.043 0.143 760 Planarity : 0.003 0.034 878 Dihedral : 4.625 51.521 778 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.12 % Allowed : 10.24 % Favored : 88.64 % 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: -0.28 (0.33), residues: 615 helix: -0.98 (1.31), residues: 20 sheet: 0.80 (0.36), residues: 208 loop : -0.72 (0.30), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 403 TYR 0.009 0.001 TYR A 189 PHE 0.009 0.001 PHE A 236 TRP 0.007 0.001 TRP A 228 HIS 0.002 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 5053) covalent geometry : angle 0.43774 ( 6850) SS BOND : bond 0.00212 ( 6) SS BOND : angle 1.69553 ( 12) hydrogen bonds : bond 0.02821 ( 127) hydrogen bonds : angle 4.92187 ( 312) link_BETA1-4 : bond 0.00314 ( 2) link_BETA1-4 : angle 1.38079 ( 6) link_NAG-ASN : bond 0.00232 ( 3) link_NAG-ASN : angle 1.39764 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1230 Ramachandran restraints generated. 615 Oldfield, 0 Emsley, 615 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 560 is missing expected H atoms. Skipping. Evaluate side-chains 54 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.258 Fit side-chains REVERT: A 108 GLN cc_start: 0.6179 (OUTLIER) cc_final: 0.5806 (pp30) REVERT: A 169 ASP cc_start: 0.7828 (m-30) cc_final: 0.7471 (m-30) REVERT: A 211 ASN cc_start: 0.8431 (t0) cc_final: 0.8185 (t0) REVERT: A 306 MET cc_start: 0.7941 (ttm) cc_final: 0.7594 (ttp) REVERT: A 546 ARG cc_start: 0.8794 (OUTLIER) cc_final: 0.8232 (ttm110) REVERT: A 582 LYS cc_start: 0.8244 (tttm) cc_final: 0.7884 (tptp) REVERT: A 623 ASP cc_start: 0.7849 (t0) cc_final: 0.7366 (t0) outliers start: 6 outliers final: 4 residues processed: 51 average time/residue: 0.2159 time to fit residues: 13.1884 Evaluate side-chains 51 residues out of total 539 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 GLN Chi-restraints excluded: chain A residue 115 GLU Chi-restraints excluded: chain A residue 220 HIS Chi-restraints excluded: chain A residue 526 THR Chi-restraints excluded: chain A residue 546 ARG Chi-restraints excluded: chain A residue 688 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 22 optimal weight: 1.9990 chunk 41 optimal weight: 0.0470 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 0.2980 chunk 12 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.4478 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.131705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.102313 restraints weight = 17175.574| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.47 r_work: 0.2953 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5064 Z= 0.084 Angle : 0.438 6.347 6877 Z= 0.232 Chirality : 0.043 0.141 760 Planarity : 0.003 0.034 878 Dihedral : 4.520 51.784 778 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 0.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.30 % Allowed : 10.24 % Favored : 88.45 % 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: -0.26 (0.33), residues: 615 helix: -0.96 (1.32), residues: 20 sheet: 0.83 (0.36), residues: 210 loop : -0.72 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 403 TYR 0.008 0.001 TYR A 189 PHE 0.009 0.001 PHE A 236 TRP 0.007 0.001 TRP A 228 HIS 0.002 0.001 HIS A 490 Details of bonding type rmsd covalent geometry : bond 0.00204 ( 5053) covalent geometry : angle 0.42999 ( 6850) SS BOND : bond 0.00205 ( 6) SS BOND : angle 1.58928 ( 12) hydrogen bonds : bond 0.02712 ( 127) hydrogen bonds : angle 4.85055 ( 312) link_BETA1-4 : bond 0.00264 ( 2) link_BETA1-4 : angle 1.30927 ( 6) link_NAG-ASN : bond 0.00245 ( 3) link_NAG-ASN : angle 1.29590 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2443.48 seconds wall clock time: 42 minutes 2.88 seconds (2522.88 seconds total)