Starting phenix.real_space_refine on Tue Aug 4 17:27:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rqn_54180/08_2026/9rqn_54180.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rqn_54180/08_2026/9rqn_54180.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rqn_54180/08_2026/9rqn_54180.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rqn_54180/08_2026/9rqn_54180.map" model { file = "/net/cci-nas-00/data/ceres_data/9rqn_54180/08_2026/9rqn_54180.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rqn_54180/08_2026/9rqn_54180.cif" } resolution = 2.94 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 28 5.16 5 C 3491 2.51 5 N 875 2.21 5 O 936 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5331 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5276 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5276 Classifications: {'peptide': 676} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PCIS': 1, 'PTRANS': 30, 'TRANS': 644} Chain breaks: 1 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 129 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 4, 'ASN:plan1': 3, 'GLN:plan1': 2, 'HIS:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 62 Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'IZY': 1, 'NAG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 1.30, per 1000 atoms: 0.24 Number of scatterers: 5331 At special positions: 0 Unit cell: (63.4326, 113.684, 102.975, 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 28 16.00 P 1 15.00 O 936 8.00 N 875 7.00 C 3491 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 522 " - pdb=" SG CYS A 544 " distance=2.02 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 NAG-ASN " NAG A 802 " - " ASN A 568 " Time building additional restraints: 0.50 Conformation dependent library (CDL) restraints added in 194.0 milliseconds 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1268 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 1 sheets defined 73.8% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 25 through 43 Processing helix chain 'A' and resid 52 through 63 Processing helix chain 'A' and resid 71 through 85 Processing helix chain 'A' and resid 89 through 118 Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.950A pdb=" N GLY A 123 " --> pdb=" O SER A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 142 removed outlier: 3.547A pdb=" N ALA A 142 " --> pdb=" O GLN A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 166 Processing helix chain 'A' and resid 168 through 187 removed outlier: 3.620A pdb=" N PHE A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 189 No H-bonds generated for 'chain 'A' and resid 188 through 189' Processing helix chain 'A' and resid 190 through 192 No H-bonds generated for 'chain 'A' and resid 190 through 192' Processing helix chain 'A' and resid 193 through 211 removed outlier: 4.357A pdb=" N CYS A 199 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Proline residue: A 202 - end of helix Processing helix chain 'A' and resid 215 through 230 removed outlier: 3.569A pdb=" N LEU A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 230 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 233 No H-bonds generated for 'chain 'A' and resid 231 through 233' Processing helix chain 'A' and resid 234 through 243 Processing helix chain 'A' and resid 254 through 263 Processing helix chain 'A' and resid 264 through 268 Processing helix chain 'A' and resid 280 through 296 removed outlier: 3.517A pdb=" N THR A 294 " --> pdb=" O THR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 311 removed outlier: 3.797A pdb=" N ASN A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 340 Processing helix chain 'A' and resid 346 through 356 removed outlier: 3.610A pdb=" N VAL A 352 " --> pdb=" O LEU A 348 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARG A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 356 " --> pdb=" O VAL A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 384 removed outlier: 3.969A pdb=" N VAL A 363 " --> pdb=" O GLN A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 388 through 412 removed outlier: 3.580A pdb=" N VAL A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N SER A 409 " --> pdb=" O TYR A 405 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N VAL A 410 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 430 Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 466 through 470 Processing helix chain 'A' and resid 472 through 478 Processing helix chain 'A' and resid 506 through 513 removed outlier: 3.678A pdb=" N VAL A 513 " --> pdb=" O HIS A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 534 removed outlier: 4.209A pdb=" N TRP A 532 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LYS A 534 " --> pdb=" O THR A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 565 removed outlier: 3.836A pdb=" N LYS A 561 " --> pdb=" O GLU A 557 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N SER A 565 " --> pdb=" O LYS A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 606 removed outlier: 3.910A pdb=" N VAL A 584 " --> pdb=" O SER A 580 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ARG A 593 " --> pdb=" O MET A 589 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N MET A 594 " --> pdb=" O TRP A 590 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS A 595 " --> pdb=" O GLN A 591 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N THR A 596 " --> pdb=" O ALA A 592 " (cutoff:3.500A) Proline residue: A 597 - end of helix Processing helix chain 'A' and resid 610 through 630 removed outlier: 3.500A pdb=" N ILE A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 653 removed outlier: 3.872A pdb=" N LYS A 641 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 678 removed outlier: 4.370A pdb=" N LEU A 663 " --> pdb=" O ASP A 659 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 665 " --> pdb=" O GLU A 661 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU A 666 " --> pdb=" O VAL A 662 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 706 Processing sheet with id=AA1, first strand: chain 'A' and resid 461 through 464 removed outlier: 5.208A pdb=" N THR A 519 " --> pdb=" O LEU A 547 " (cutoff:3.500A) 349 hydrogen bonds defined for protein. 1029 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: 0.67 Time building geometry restraints manager: 0.66 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1445 1.34 - 1.46: 1190 1.46 - 1.58: 2803 1.58 - 1.70: 0 1.70 - 1.82: 42 Bond restraints: 5480 Sorted by residual: bond pdb=" C02 IZY A 801 " pdb=" C03 IZY A 801 " ideal model delta sigma weight residual 1.502 1.345 0.157 2.00e-02 2.50e+03 6.13e+01 bond pdb=" O30 IZY A 801 " pdb=" P27 IZY A 801 " ideal model delta sigma weight residual 1.665 1.563 0.102 2.00e-02 2.50e+03 2.59e+01 bond pdb=" O26 IZY A 801 " pdb=" P27 IZY A 801 " ideal model delta sigma weight residual 1.635 1.557 0.078 2.00e-02 2.50e+03 1.53e+01 bond pdb=" C31 IZY A 801 " pdb=" O30 IZY A 801 " ideal model delta sigma weight residual 1.381 1.450 -0.069 2.00e-02 2.50e+03 1.18e+01 bond pdb=" CA ALA A 35 " pdb=" CB ALA A 35 " ideal model delta sigma weight residual 1.529 1.573 -0.044 1.62e-02 3.81e+03 7.35e+00 ... (remaining 5475 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 7353 3.00 - 5.99: 101 5.99 - 8.99: 7 8.99 - 11.99: 0 11.99 - 14.98: 1 Bond angle restraints: 7462 Sorted by residual: angle pdb=" O28 IZY A 801 " pdb=" P27 IZY A 801 " pdb=" O29 IZY A 801 " ideal model delta sigma weight residual 122.89 107.91 14.98 3.00e+00 1.11e-01 2.49e+01 angle pdb=" N ASN A 425 " pdb=" CA ASN A 425 " pdb=" C ASN A 425 " ideal model delta sigma weight residual 111.33 116.46 -5.13 1.21e+00 6.83e-01 1.79e+01 angle pdb=" N SER A 227 " pdb=" CA SER A 227 " pdb=" C SER A 227 " ideal model delta sigma weight residual 112.89 108.18 4.71 1.24e+00 6.50e-01 1.44e+01 angle pdb=" N VAL A 234 " pdb=" CA VAL A 234 " pdb=" C VAL A 234 " ideal model delta sigma weight residual 113.00 108.79 4.21 1.30e+00 5.92e-01 1.05e+01 angle pdb=" N LEU A 272 " pdb=" CA LEU A 272 " pdb=" C LEU A 272 " ideal model delta sigma weight residual 112.88 108.79 4.09 1.29e+00 6.01e-01 1.00e+01 ... (remaining 7457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.31: 3160 29.31 - 58.62: 60 58.62 - 87.93: 7 87.93 - 117.24: 0 117.24 - 146.55: 1 Dihedral angle restraints: 3228 sinusoidal: 1260 harmonic: 1968 Sorted by residual: dihedral pdb=" C07 IZY A 801 " pdb=" C09 IZY A 801 " pdb=" C10 IZY A 801 " pdb=" C11 IZY A 801 " ideal model delta sinusoidal sigma weight residual 105.02 -108.43 -146.55 1 3.00e+01 1.11e-03 1.96e+01 dihedral pdb=" C SER A 227 " pdb=" N SER A 227 " pdb=" CA SER A 227 " pdb=" CB SER A 227 " ideal model delta harmonic sigma weight residual -122.60 -112.44 -10.16 0 2.50e+00 1.60e-01 1.65e+01 dihedral pdb=" C ARG A 593 " pdb=" N ARG A 593 " pdb=" CA ARG A 593 " pdb=" CB ARG A 593 " ideal model delta harmonic sigma weight residual -122.60 -112.74 -9.86 0 2.50e+00 1.60e-01 1.56e+01 ... (remaining 3225 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 608 0.091 - 0.182: 168 0.182 - 0.272: 44 0.272 - 0.363: 15 0.363 - 0.454: 3 Chirality restraints: 838 Sorted by residual: chirality pdb=" CA SER A 227 " pdb=" N SER A 227 " pdb=" C SER A 227 " pdb=" CB SER A 227 " both_signs ideal model delta sigma weight residual False 2.51 2.96 -0.45 2.00e-01 2.50e+01 5.15e+00 chirality pdb=" CA ARG A 593 " pdb=" N ARG A 593 " pdb=" C ARG A 593 " pdb=" CB ARG A 593 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA PHE A 146 " pdb=" N PHE A 146 " pdb=" C PHE A 146 " pdb=" CB PHE A 146 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.33e+00 ... (remaining 835 not shown) Planarity restraints: 930 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C06 IZY A 801 " -0.190 2.00e-02 2.50e+03 2.42e-01 7.30e+02 pdb=" C07 IZY A 801 " 0.090 2.00e-02 2.50e+03 pdb=" C08 IZY A 801 " -0.020 2.00e-02 2.50e+03 pdb=" C09 IZY A 801 " 0.406 2.00e-02 2.50e+03 pdb=" C10 IZY A 801 " -0.287 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 IZY A 801 " 0.025 2.00e-02 2.50e+03 1.60e-01 3.18e+02 pdb=" C02 IZY A 801 " 0.045 2.00e-02 2.50e+03 pdb=" C03 IZY A 801 " -0.146 2.00e-02 2.50e+03 pdb=" C04 IZY A 801 " 0.262 2.00e-02 2.50e+03 pdb=" C05 IZY A 801 " -0.186 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 IZY A 801 " -0.137 2.00e-02 2.50e+03 1.55e-01 2.99e+02 pdb=" C17 IZY A 801 " 0.061 2.00e-02 2.50e+03 pdb=" C18 IZY A 801 " 0.008 2.00e-02 2.50e+03 pdb=" C19 IZY A 801 " 0.251 2.00e-02 2.50e+03 pdb=" C20 IZY A 801 " -0.184 2.00e-02 2.50e+03 ... (remaining 927 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 337 2.74 - 3.28: 5704 3.28 - 3.82: 8908 3.82 - 4.36: 11017 4.36 - 4.90: 18771 Nonbonded interactions: 44737 Sorted by model distance: nonbonded pdb=" OH TYR A 643 " pdb=" OE1 GLU A 666 " model vdw 2.196 3.040 nonbonded pdb=" O PRO A 475 " pdb=" NZ LYS A 479 " model vdw 2.247 3.120 nonbonded pdb=" OH TYR A 573 " pdb=" OE1 GLU A 587 " model vdw 2.313 3.040 nonbonded pdb=" O ILE A 284 " pdb=" OG SER A 287 " model vdw 2.324 3.040 nonbonded pdb=" O ILE A 628 " pdb=" NE2 GLN A 632 " model vdw 2.333 3.120 ... (remaining 44732 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.090 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: 0.000 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.370 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.157 5482 Z= 0.435 Angle : 0.935 14.984 7467 Z= 0.559 Chirality : 0.098 0.454 838 Planarity : 0.016 0.242 929 Dihedral : 12.411 146.552 1957 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.62 % Rotamer: Outliers : 0.18 % Allowed : 4.20 % Favored : 95.62 % Cbeta Deviations : 0.32 % Peptide Plane: Cis-proline : 3.33 % 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 (0.30), residues: 672 helix: 0.09 (0.23), residues: 431 sheet: 0.91 (1.00), residues: 27 loop : -0.77 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.062 0.008 ARG A 355 TYR 0.054 0.007 TYR A 618 PHE 0.042 0.004 PHE A 349 TRP 0.058 0.004 TRP A 338 HIS 0.018 0.004 HIS A 61 Details of bonding type rmsd/Z covalent geometry : bond 0.00704 / 0.44 ( 5480) covalent geometry : angle 0.93278 / 0.56 ( 7462) SS BOND : bond 0.00940 / 0.59 ( 1) SS BOND : angle 1.05838 / 0.50 ( 2) hydrogen bonds : bond 0.22750 / 15.78 ( 349) hydrogen bonds : angle 6.53189 / 4.76 ( 1029) link_NAG-ASN : bond 0.00097 / 0.06 ( 1) link_NAG-ASN : angle 3.22841 / 1.93 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.129 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 65 average time/residue: 0.5382 time to fit residues: 36.3608 Evaluate side-chains 33 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS A 190 GLN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 602 ASN A 640 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.092174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.075355 restraints weight = 10702.300| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.62 r_work: 0.2963 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5482 Z= 0.150 Angle : 0.574 6.253 7467 Z= 0.288 Chirality : 0.042 0.141 838 Planarity : 0.005 0.040 929 Dihedral : 9.859 179.800 794 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.79 % Favored : 98.07 % Rotamer: Outliers : 1.28 % Allowed : 8.76 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.32), residues: 672 helix: 1.80 (0.24), residues: 450 sheet: 1.08 (1.01), residues: 27 loop : -0.37 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 575 TYR 0.009 0.001 TYR A 473 PHE 0.012 0.001 PHE A 422 TRP 0.012 0.001 TRP A 139 HIS 0.011 0.002 HIS A 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 5480) covalent geometry : angle 0.57323 / 0.29 ( 7462) SS BOND : bond 0.00130 / 0.08 ( 1) SS BOND : angle 0.97084 / 0.46 ( 2) hydrogen bonds : bond 0.04397 / 3.03 ( 349) hydrogen bonds : angle 4.41023 / 3.17 ( 1029) link_NAG-ASN : bond 0.00240 / 0.15 ( 1) link_NAG-ASN : angle 1.02703 / 0.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.160 Fit side-chains REVERT: A 55 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7534 (tt0) REVERT: A 350 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7346 (tpp) REVERT: A 508 TYR cc_start: 0.8087 (t80) cc_final: 0.7831 (t80) outliers start: 7 outliers final: 0 residues processed: 39 average time/residue: 0.4003 time to fit residues: 16.5574 Evaluate side-chains 32 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 350 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 308 ASN A 693 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.086928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.069240 restraints weight = 10947.964| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.63 r_work: 0.2836 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5482 Z= 0.163 Angle : 0.532 8.945 7467 Z= 0.267 Chirality : 0.042 0.158 838 Planarity : 0.004 0.042 929 Dihedral : 8.925 174.650 794 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.64 % Favored : 98.21 % Rotamer: Outliers : 1.46 % Allowed : 8.94 % Favored : 89.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.89 (0.32), residues: 672 helix: 1.96 (0.24), residues: 453 sheet: 0.61 (0.99), residues: 27 loop : -0.33 (0.44), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 669 TYR 0.009 0.001 TYR A 408 PHE 0.012 0.001 PHE A 262 TRP 0.010 0.001 TRP A 139 HIS 0.010 0.001 HIS A 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 ( 5480) covalent geometry : angle 0.53200 / 0.27 ( 7462) SS BOND : bond 0.00234 / 0.15 ( 1) SS BOND : angle 0.99939 / 0.47 ( 2) hydrogen bonds : bond 0.04503 / 3.14 ( 349) hydrogen bonds : angle 4.09314 / 2.95 ( 1029) link_NAG-ASN : bond 0.00136 / 0.08 ( 1) link_NAG-ASN : angle 1.01531 / 0.56 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.162 Fit side-chains REVERT: A 55 GLU cc_start: 0.8110 (OUTLIER) cc_final: 0.7625 (tt0) REVERT: A 270 PHE cc_start: 0.7904 (m-80) cc_final: 0.7633 (m-80) REVERT: A 291 ASN cc_start: 0.8197 (m-40) cc_final: 0.7668 (m110) REVERT: A 348 LEU cc_start: 0.8564 (mm) cc_final: 0.8356 (mm) REVERT: A 450 MET cc_start: 0.8598 (mmt) cc_final: 0.8390 (mmt) REVERT: A 703 ASN cc_start: 0.9327 (m110) cc_final: 0.9114 (m110) outliers start: 8 outliers final: 2 residues processed: 37 average time/residue: 0.3422 time to fit residues: 13.5479 Evaluate side-chains 32 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 350 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 61 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 5 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.086876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.069073 restraints weight = 10922.652| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.62 r_work: 0.2821 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5482 Z= 0.133 Angle : 0.484 6.909 7467 Z= 0.241 Chirality : 0.040 0.143 838 Planarity : 0.004 0.043 929 Dihedral : 8.565 168.464 794 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.93 % Favored : 97.92 % Rotamer: Outliers : 1.09 % Allowed : 9.49 % Favored : 89.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.06 (0.32), residues: 672 helix: 2.15 (0.24), residues: 452 sheet: 0.36 (0.93), residues: 27 loop : -0.35 (0.44), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.006 0.001 TYR A 408 PHE 0.009 0.001 PHE A 422 TRP 0.008 0.001 TRP A 139 HIS 0.006 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.13 ( 5480) covalent geometry : angle 0.48329 / 0.24 ( 7462) SS BOND : bond 0.00216 / 0.14 ( 1) SS BOND : angle 0.97718 / 0.46 ( 2) hydrogen bonds : bond 0.03777 / 2.62 ( 349) hydrogen bonds : angle 3.94035 / 2.83 ( 1029) link_NAG-ASN : bond 0.00060 / 0.04 ( 1) link_NAG-ASN : angle 0.91112 / 0.48 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.167 Fit side-chains REVERT: A 55 GLU cc_start: 0.8123 (OUTLIER) cc_final: 0.7674 (tt0) REVERT: A 270 PHE cc_start: 0.7916 (m-80) cc_final: 0.7658 (m-80) REVERT: A 291 ASN cc_start: 0.8255 (m-40) cc_final: 0.7771 (m110) REVERT: A 348 LEU cc_start: 0.8532 (mm) cc_final: 0.8324 (mm) REVERT: A 350 MET cc_start: 0.7725 (OUTLIER) cc_final: 0.7436 (tpp) REVERT: A 703 ASN cc_start: 0.9360 (m110) cc_final: 0.9121 (m110) outliers start: 6 outliers final: 2 residues processed: 36 average time/residue: 0.3636 time to fit residues: 14.0577 Evaluate side-chains 33 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 350 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 62 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.067441 restraints weight = 11246.173| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 2.64 r_work: 0.2795 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5482 Z= 0.151 Angle : 0.496 8.066 7467 Z= 0.246 Chirality : 0.040 0.161 838 Planarity : 0.004 0.045 929 Dihedral : 8.385 168.115 794 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.62 % Rotamer: Outliers : 0.91 % Allowed : 10.22 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.32), residues: 672 helix: 2.18 (0.24), residues: 452 sheet: 0.77 (1.35), residues: 17 loop : -0.32 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 575 TYR 0.007 0.001 TYR A 408 PHE 0.010 0.001 PHE A 422 TRP 0.007 0.001 TRP A 139 HIS 0.006 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 ( 5480) covalent geometry : angle 0.49544 / 0.25 ( 7462) SS BOND : bond 0.00301 / 0.19 ( 1) SS BOND : angle 1.07238 / 0.49 ( 2) hydrogen bonds : bond 0.03955 / 2.75 ( 349) hydrogen bonds : angle 3.93608 / 2.82 ( 1029) link_NAG-ASN : bond 0.00064 / 0.04 ( 1) link_NAG-ASN : angle 0.92337 / 0.49 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.186 Fit side-chains REVERT: A 55 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7713 (tt0) REVERT: A 291 ASN cc_start: 0.8285 (m-40) cc_final: 0.7801 (m110) REVERT: A 350 MET cc_start: 0.7698 (OUTLIER) cc_final: 0.7420 (tpp) REVERT: A 477 MET cc_start: 0.8313 (mmm) cc_final: 0.8080 (mtp) REVERT: A 672 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.7102 (ptt-90) REVERT: A 703 ASN cc_start: 0.9406 (m110) cc_final: 0.9149 (m110) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 0.3313 time to fit residues: 11.7112 Evaluate side-chains 33 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 672 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 24 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 49 optimal weight: 0.0010 chunk 51 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.3980 chunk 42 optimal weight: 2.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.086554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.068875 restraints weight = 11165.988| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 2.63 r_work: 0.2828 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.4140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5482 Z= 0.105 Angle : 0.450 7.824 7467 Z= 0.222 Chirality : 0.039 0.139 838 Planarity : 0.004 0.044 929 Dihedral : 8.072 164.579 794 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.79 % Favored : 98.07 % Rotamer: Outliers : 0.91 % Allowed : 10.04 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.32), residues: 672 helix: 2.30 (0.24), residues: 455 sheet: 0.52 (1.32), residues: 17 loop : -0.22 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.005 0.001 TYR A 417 PHE 0.008 0.001 PHE A 422 TRP 0.007 0.001 TRP A 139 HIS 0.005 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 ( 5480) covalent geometry : angle 0.44913 / 0.22 ( 7462) SS BOND : bond 0.00250 / 0.16 ( 1) SS BOND : angle 0.90306 / 0.42 ( 2) hydrogen bonds : bond 0.03378 / 2.34 ( 349) hydrogen bonds : angle 3.77707 / 2.71 ( 1029) link_NAG-ASN : bond 0.00159 / 0.10 ( 1) link_NAG-ASN : angle 0.81400 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.120 Fit side-chains REVERT: A 55 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7739 (tt0) REVERT: A 291 ASN cc_start: 0.8248 (m-40) cc_final: 0.7795 (m110) REVERT: A 350 MET cc_start: 0.7671 (OUTLIER) cc_final: 0.7422 (tpp) REVERT: A 477 MET cc_start: 0.8302 (mmm) cc_final: 0.8070 (mtp) REVERT: A 650 MET cc_start: 0.8024 (mmm) cc_final: 0.7804 (mmt) REVERT: A 703 ASN cc_start: 0.9429 (m110) cc_final: 0.9187 (m-40) outliers start: 5 outliers final: 1 residues processed: 34 average time/residue: 0.3618 time to fit residues: 13.1162 Evaluate side-chains 32 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 350 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.085510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.067587 restraints weight = 11253.863| |-----------------------------------------------------------------------------| r_work (start): 0.2936 rms_B_bonded: 2.68 r_work: 0.2800 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.4248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5482 Z= 0.134 Angle : 0.474 7.594 7467 Z= 0.235 Chirality : 0.040 0.168 838 Planarity : 0.004 0.044 929 Dihedral : 8.081 165.435 794 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.23 % Favored : 97.62 % Rotamer: Outliers : 0.91 % Allowed : 10.58 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.33), residues: 672 helix: 2.31 (0.24), residues: 454 sheet: 0.43 (1.32), residues: 17 loop : -0.24 (0.42), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.008 0.001 TYR A 267 PHE 0.010 0.001 PHE A 422 TRP 0.006 0.001 TRP A 139 HIS 0.005 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 ( 5480) covalent geometry : angle 0.47370 / 0.23 ( 7462) SS BOND : bond 0.00301 / 0.19 ( 1) SS BOND : angle 0.94085 / 0.42 ( 2) hydrogen bonds : bond 0.03650 / 2.55 ( 349) hydrogen bonds : angle 3.81633 / 2.73 ( 1029) link_NAG-ASN : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : angle 0.89570 / 0.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.122 Fit side-chains REVERT: A 55 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.7861 (tt0) REVERT: A 291 ASN cc_start: 0.8289 (m-40) cc_final: 0.7804 (m110) REVERT: A 350 MET cc_start: 0.7713 (OUTLIER) cc_final: 0.7445 (tpp) REVERT: A 477 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.8207 (mtp) REVERT: A 650 MET cc_start: 0.8065 (mmm) cc_final: 0.7804 (mmt) REVERT: A 672 ARG cc_start: 0.7300 (OUTLIER) cc_final: 0.7049 (ptt-90) REVERT: A 703 ASN cc_start: 0.9451 (m110) cc_final: 0.9195 (m-40) outliers start: 5 outliers final: 1 residues processed: 31 average time/residue: 0.3781 time to fit residues: 12.4812 Evaluate side-chains 33 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 672 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 47 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.086066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.068240 restraints weight = 11077.296| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 2.65 r_work: 0.2809 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5482 Z= 0.116 Angle : 0.458 7.242 7467 Z= 0.227 Chirality : 0.039 0.169 838 Planarity : 0.004 0.045 929 Dihedral : 7.996 164.898 794 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.93 % Favored : 97.92 % Rotamer: Outliers : 0.91 % Allowed : 10.58 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.33), residues: 672 helix: 2.36 (0.24), residues: 454 sheet: 0.33 (1.31), residues: 17 loop : -0.23 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 669 TYR 0.007 0.001 TYR A 267 PHE 0.009 0.001 PHE A 422 TRP 0.007 0.001 TRP A 139 HIS 0.005 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5480) covalent geometry : angle 0.45760 / 0.23 ( 7462) SS BOND : bond 0.00281 / 0.18 ( 1) SS BOND : angle 0.98825 / 0.46 ( 2) hydrogen bonds : bond 0.03473 / 2.42 ( 349) hydrogen bonds : angle 3.76625 / 2.69 ( 1029) link_NAG-ASN : bond 0.00138 / 0.09 ( 1) link_NAG-ASN : angle 0.81988 / 0.43 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.133 Fit side-chains REVERT: A 55 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: A 220 LEU cc_start: 0.6978 (mt) cc_final: 0.6654 (tp) REVERT: A 291 ASN cc_start: 0.8290 (m-40) cc_final: 0.7822 (m110) REVERT: A 350 MET cc_start: 0.7704 (OUTLIER) cc_final: 0.7462 (tpp) REVERT: A 477 MET cc_start: 0.8394 (OUTLIER) cc_final: 0.8154 (mtp) REVERT: A 672 ARG cc_start: 0.7333 (OUTLIER) cc_final: 0.7107 (ptt-90) REVERT: A 702 ARG cc_start: 0.9308 (mmm160) cc_final: 0.8830 (mmm160) outliers start: 5 outliers final: 1 residues processed: 34 average time/residue: 0.3417 time to fit residues: 12.4070 Evaluate side-chains 34 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 477 MET Chi-restraints excluded: chain A residue 672 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 52 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 699 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.085395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.067552 restraints weight = 11177.261| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.66 r_work: 0.2794 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.4385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5482 Z= 0.130 Angle : 0.475 8.705 7467 Z= 0.235 Chirality : 0.040 0.160 838 Planarity : 0.004 0.045 929 Dihedral : 8.018 165.298 794 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.38 % Favored : 97.47 % Rotamer: Outliers : 0.91 % Allowed : 10.58 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.33), residues: 672 helix: 2.34 (0.24), residues: 454 sheet: 0.14 (1.28), residues: 17 loop : -0.23 (0.43), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.007 0.001 TYR A 449 PHE 0.010 0.001 PHE A 422 TRP 0.006 0.001 TRP A 139 HIS 0.005 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 5480) covalent geometry : angle 0.47415 / 0.23 ( 7462) SS BOND : bond 0.00282 / 0.18 ( 1) SS BOND : angle 0.96271 / 0.45 ( 2) hydrogen bonds : bond 0.03640 / 2.54 ( 349) hydrogen bonds : angle 3.81725 / 2.74 ( 1029) link_NAG-ASN : bond 0.00070 / 0.04 ( 1) link_NAG-ASN : angle 0.86472 / 0.44 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.125 Fit side-chains REVERT: A 55 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: A 220 LEU cc_start: 0.7011 (mt) cc_final: 0.6690 (tp) REVERT: A 291 ASN cc_start: 0.8301 (m-40) cc_final: 0.7808 (m110) REVERT: A 350 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7432 (tpp) REVERT: A 672 ARG cc_start: 0.7364 (OUTLIER) cc_final: 0.7143 (ptt-90) outliers start: 5 outliers final: 1 residues processed: 33 average time/residue: 0.3208 time to fit residues: 11.2712 Evaluate side-chains 33 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 350 MET Chi-restraints excluded: chain A residue 672 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.0970 chunk 3 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 60 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.086620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.068876 restraints weight = 11286.333| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.64 r_work: 0.2824 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.4439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5482 Z= 0.101 Angle : 0.452 8.241 7467 Z= 0.223 Chirality : 0.039 0.161 838 Planarity : 0.004 0.044 929 Dihedral : 7.926 164.067 794 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.93 % Favored : 97.92 % Rotamer: Outliers : 0.73 % Allowed : 11.13 % Favored : 88.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.32), residues: 672 helix: 2.33 (0.24), residues: 461 sheet: 0.21 (1.27), residues: 17 loop : -0.11 (0.43), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 575 TYR 0.005 0.001 TYR A 267 PHE 0.008 0.001 PHE A 422 TRP 0.006 0.001 TRP A 139 HIS 0.005 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 5480) covalent geometry : angle 0.45176 / 0.22 ( 7462) SS BOND : bond 0.00253 / 0.16 ( 1) SS BOND : angle 0.82531 / 0.38 ( 2) hydrogen bonds : bond 0.03334 / 2.31 ( 349) hydrogen bonds : angle 3.74730 / 2.70 ( 1029) link_NAG-ASN : bond 0.00154 / 0.10 ( 1) link_NAG-ASN : angle 0.77661 / 0.40 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1344 Ramachandran restraints generated. 672 Oldfield, 0 Emsley, 672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.128 Fit side-chains REVERT: A 55 GLU cc_start: 0.8245 (OUTLIER) cc_final: 0.7888 (tt0) REVERT: A 220 LEU cc_start: 0.7044 (mt) cc_final: 0.6714 (tp) REVERT: A 291 ASN cc_start: 0.8306 (m-40) cc_final: 0.7832 (m110) REVERT: A 350 MET cc_start: 0.7656 (OUTLIER) cc_final: 0.7436 (tpp) outliers start: 4 outliers final: 1 residues processed: 33 average time/residue: 0.3767 time to fit residues: 13.2645 Evaluate side-chains 31 residues out of total 578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 GLU Chi-restraints excluded: chain A residue 334 LEU Chi-restraints excluded: chain A residue 350 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 42 optimal weight: 0.2980 chunk 62 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.086203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.068458 restraints weight = 11148.155| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 2.64 r_work: 0.2816 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.4459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5482 Z= 0.114 Angle : 0.473 8.328 7467 Z= 0.232 Chirality : 0.039 0.172 838 Planarity : 0.004 0.045 929 Dihedral : 7.919 163.926 794 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.53 % Favored : 97.32 % Rotamer: Outliers : 0.73 % Allowed : 11.31 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.34 (0.32), residues: 672 helix: 2.30 (0.24), residues: 462 sheet: 0.19 (1.27), residues: 17 loop : -0.14 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 672 TYR 0.006 0.001 TYR A 267 PHE 0.009 0.001 PHE A 422 TRP 0.007 0.001 TRP A 247 HIS 0.005 0.001 HIS A 670 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.11 ( 5480) covalent geometry : angle 0.47259 / 0.23 ( 7462) SS BOND : bond 0.00277 / 0.17 ( 1) SS BOND : angle 0.92375 / 0.41 ( 2) hydrogen bonds : bond 0.03441 / 2.38 ( 349) hydrogen bonds : angle 3.75926 / 2.71 ( 1029) link_NAG-ASN : bond 0.00118 / 0.07 ( 1) link_NAG-ASN : angle 0.80450 / 0.42 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1196.78 seconds wall clock time: 21 minutes 10.95 seconds (1270.95 seconds total)