Starting phenix.real_space_refine on Fri May 9 19:06:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3u_35156/05_2025/8i3u_35156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3u_35156/05_2025/8i3u_35156.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i3u_35156/05_2025/8i3u_35156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3u_35156/05_2025/8i3u_35156.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3u_35156/05_2025/8i3u_35156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3u_35156/05_2025/8i3u_35156.cif" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.036 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2161 2.51 5 N 579 2.21 5 O 652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3408 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1552 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1028 Classifications: {'peptide': 133} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 128} Chain: "L" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 814 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} 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: 3.40, per 1000 atoms: 1.00 Number of scatterers: 3408 At special positions: 0 Unit cell: (63.65, 61.75, 106.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 652 8.00 N 579 7.00 C 2161 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.39 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " 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 NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 357.8 milliseconds 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 9 sheets defined 10.3% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.575A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.117A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 388 removed outlier: 4.339A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 3.644A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.551A pdb=" N ILE H 87 " --> pdb=" O SER H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.525A pdb=" N THR H 68 " --> pdb=" O GLN H 81 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA6, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.614A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.744A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AA9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.427A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 102 hydrogen bonds defined for protein. 255 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: 0.78 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1100 1.34 - 1.46: 903 1.46 - 1.58: 1473 1.58 - 1.70: 0 1.70 - 1.81: 20 Bond restraints: 3496 Sorted by residual: bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 1.469 1.484 -0.015 1.28e-02 6.10e+03 1.42e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C3 NAG A1301 " pdb=" O3 NAG A1301 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.03e+00 bond pdb=" CA ILE A 410 " pdb=" CB ILE A 410 " ideal model delta sigma weight residual 1.527 1.538 -0.012 1.31e-02 5.83e+03 7.90e-01 ... (remaining 3491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 4629 1.35 - 2.71: 89 2.71 - 4.06: 22 4.06 - 5.41: 8 5.41 - 6.76: 1 Bond angle restraints: 4749 Sorted by residual: angle pdb=" C PRO L 95 " pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta sigma weight residual 119.84 113.08 6.76 1.25e+00 6.40e-01 2.93e+01 angle pdb=" N PRO L 95 " pdb=" CA PRO L 95 " pdb=" C PRO L 95 " ideal model delta sigma weight residual 110.70 114.12 -3.42 1.22e+00 6.72e-01 7.84e+00 angle pdb=" CA PRO L 95 " pdb=" C PRO L 95 " pdb=" N PRO L 95A" ideal model delta sigma weight residual 117.93 120.61 -2.68 1.20e+00 6.94e-01 4.98e+00 angle pdb=" C VAL H 48 " pdb=" N SER H 49 " pdb=" CA SER H 49 " ideal model delta sigma weight residual 122.21 118.76 3.45 1.62e+00 3.81e-01 4.53e+00 angle pdb=" C GLY A 476 " pdb=" N SER A 477 " pdb=" CA SER A 477 " ideal model delta sigma weight residual 121.54 125.09 -3.55 1.91e+00 2.74e-01 3.46e+00 ... (remaining 4744 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.54: 1865 11.54 - 23.08: 136 23.08 - 34.61: 46 34.61 - 46.15: 10 46.15 - 57.69: 2 Dihedral angle restraints: 2059 sinusoidal: 812 harmonic: 1247 Sorted by residual: dihedral pdb=" CA PRO L 95 " pdb=" C PRO L 95 " pdb=" N PRO L 95A" pdb=" CA PRO L 95A" ideal model delta harmonic sigma weight residual 180.00 159.73 20.27 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA TYR H 91 " pdb=" C TYR H 91 " pdb=" N CYS H 92 " pdb=" CA CYS H 92 " ideal model delta harmonic sigma weight residual 180.00 161.04 18.96 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 118.67 -25.67 1 1.00e+01 1.00e-02 9.48e+00 ... (remaining 2056 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 301 0.027 - 0.053: 126 0.053 - 0.080: 29 0.080 - 0.106: 37 0.106 - 0.132: 12 Chirality restraints: 505 Sorted by residual: chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA GLU H 26 " pdb=" N GLU H 26 " pdb=" C GLU H 26 " pdb=" CB GLU H 26 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA VAL A 382 " pdb=" N VAL A 382 " pdb=" C VAL A 382 " pdb=" CB VAL A 382 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.64e-01 ... (remaining 502 not shown) Planarity restraints: 621 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO L 95 " -0.058 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO L 95A" 0.152 5.00e-02 4.00e+02 pdb=" CA PRO L 95A" -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 95A" -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP L 94 " 0.030 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO L 95 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " 0.018 5.00e-02 4.00e+02 2.73e-02 1.20e+00 pdb=" N PRO A 491 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " 0.015 5.00e-02 4.00e+02 ... (remaining 618 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 221 2.74 - 3.28: 3219 3.28 - 3.82: 5418 3.82 - 4.36: 6360 4.36 - 4.90: 11589 Nonbonded interactions: 26807 Sorted by model distance: nonbonded pdb=" O HIS L 49 " pdb=" OG1 THR L 53 " model vdw 2.198 3.040 nonbonded pdb=" OD2 ASP A 398 " pdb=" OH TYR A 423 " model vdw 2.268 3.040 nonbonded pdb=" NZ LYS A 417 " pdb=" OD2 ASP H 31 " model vdw 2.289 3.120 nonbonded pdb=" O ILE H 29 " pdb=" NH2 ARG H 71 " model vdw 2.308 3.120 nonbonded pdb=" NH2 ARG A 454 " pdb=" O SER A 469 " model vdw 2.319 3.120 ... (remaining 26802 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.780 Find NCS groups from input model: 0.030 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 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 0.363 3502 Z= 0.331 Angle : 0.641 23.216 4762 Z= 0.343 Chirality : 0.041 0.132 505 Planarity : 0.005 0.088 620 Dihedral : 9.198 57.687 1258 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.09 % Allowed : 5.72 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.41), residues: 431 helix: -1.62 (0.94), residues: 27 sheet: 0.02 (0.46), residues: 132 loop : -0.34 (0.39), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 PHE 0.006 0.001 PHE A 456 TYR 0.011 0.001 TYR L 91 ARG 0.001 0.000 ARG L 18 Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 1) link_NAG-ASN : angle 0.96077 ( 3) hydrogen bonds : bond 0.17501 ( 102) hydrogen bonds : angle 9.43176 ( 255) SS BOND : bond 0.16245 ( 5) SS BOND : angle 7.71965 ( 10) covalent geometry : bond 0.00245 ( 3496) covalent geometry : angle 0.53518 ( 4749) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.401 Fit side-chains REVERT: A 392 PHE cc_start: 0.7569 (m-80) cc_final: 0.7264 (m-80) REVERT: A 444 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8073 (mtmm) REVERT: H 34 MET cc_start: 0.8171 (mmm) cc_final: 0.7867 (mmm) REVERT: L 29 ILE cc_start: 0.7289 (mm) cc_final: 0.7057 (mm) outliers start: 4 outliers final: 0 residues processed: 115 average time/residue: 0.1891 time to fit residues: 25.5849 Evaluate side-chains 81 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 ASN L 93 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.155810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.130696 restraints weight = 4375.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134365 restraints weight = 2685.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.136878 restraints weight = 1955.414| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 3502 Z= 0.207 Angle : 0.618 8.520 4762 Z= 0.316 Chirality : 0.043 0.160 505 Planarity : 0.006 0.093 620 Dihedral : 5.038 26.659 505 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.54 % Allowed : 14.17 % Favored : 82.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.56 (0.41), residues: 431 helix: -1.29 (1.01), residues: 28 sheet: 0.10 (0.48), residues: 124 loop : -0.46 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.016 0.001 PHE A 342 TYR 0.019 0.002 TYR L 91 ARG 0.005 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00169 ( 1) link_NAG-ASN : angle 1.08068 ( 3) hydrogen bonds : bond 0.03861 ( 102) hydrogen bonds : angle 7.06750 ( 255) SS BOND : bond 0.00498 ( 5) SS BOND : angle 1.12441 ( 10) covalent geometry : bond 0.00488 ( 3496) covalent geometry : angle 0.61596 ( 4749) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.362 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1883 time to fit residues: 21.5948 Evaluate side-chains 93 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 83 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 0.0040 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 overall best weight: 0.4406 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 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 = 0.4035 r_free = 0.4035 target = 0.167210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.141923 restraints weight = 4123.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.145939 restraints weight = 2532.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.148688 restraints weight = 1843.797| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3502 Z= 0.140 Angle : 0.575 8.148 4762 Z= 0.289 Chirality : 0.042 0.145 505 Planarity : 0.005 0.085 620 Dihedral : 4.740 22.903 505 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.81 % Allowed : 15.53 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.41), residues: 431 helix: -1.28 (1.03), residues: 28 sheet: 0.29 (0.47), residues: 129 loop : -0.50 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE H 27 TYR 0.014 0.001 TYR L 91 ARG 0.004 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 1) link_NAG-ASN : angle 0.98772 ( 3) hydrogen bonds : bond 0.03117 ( 102) hydrogen bonds : angle 6.70340 ( 255) SS BOND : bond 0.00265 ( 5) SS BOND : angle 1.17317 ( 10) covalent geometry : bond 0.00335 ( 3496) covalent geometry : angle 0.57276 ( 4749) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.349 Fit side-chains REVERT: A 365 TYR cc_start: 0.7723 (m-80) cc_final: 0.7512 (m-80) REVERT: A 468 ILE cc_start: 0.9137 (pt) cc_final: 0.8767 (mt) outliers start: 14 outliers final: 12 residues processed: 90 average time/residue: 0.1787 time to fit residues: 19.0744 Evaluate side-chains 92 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 56 THR Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 102 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 24 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.4980 chunk 14 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.161041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.135702 restraints weight = 4494.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.139486 restraints weight = 2759.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.142133 restraints weight = 1998.118| |-----------------------------------------------------------------------------| r_work (final): 0.3701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3502 Z= 0.170 Angle : 0.613 9.251 4762 Z= 0.301 Chirality : 0.042 0.146 505 Planarity : 0.006 0.092 620 Dihedral : 4.802 23.964 505 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.90 % Allowed : 16.89 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.41), residues: 431 helix: -1.33 (1.00), residues: 28 sheet: 0.44 (0.48), residues: 127 loop : -0.63 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.012 0.001 PHE H 27 TYR 0.012 0.001 TYR L 91 ARG 0.005 0.001 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00163 ( 1) link_NAG-ASN : angle 1.16978 ( 3) hydrogen bonds : bond 0.03050 ( 102) hydrogen bonds : angle 6.52972 ( 255) SS BOND : bond 0.00317 ( 5) SS BOND : angle 1.05802 ( 10) covalent geometry : bond 0.00405 ( 3496) covalent geometry : angle 0.61128 ( 4749) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 0.315 Fit side-chains REVERT: A 365 TYR cc_start: 0.7926 (m-80) cc_final: 0.7645 (m-80) REVERT: A 468 ILE cc_start: 0.9117 (pt) cc_final: 0.8750 (mt) outliers start: 18 outliers final: 15 residues processed: 89 average time/residue: 0.1929 time to fit residues: 20.2023 Evaluate side-chains 93 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 445 VAL Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 0.0670 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 14 optimal weight: 0.0270 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.167941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.142790 restraints weight = 4192.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.146780 restraints weight = 2614.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.149115 restraints weight = 1909.115| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3502 Z= 0.130 Angle : 0.568 9.156 4762 Z= 0.278 Chirality : 0.042 0.141 505 Planarity : 0.005 0.088 620 Dihedral : 4.633 22.937 505 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.27 % Allowed : 20.44 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.41), residues: 431 helix: -1.24 (1.03), residues: 28 sheet: 0.47 (0.48), residues: 129 loop : -0.62 (0.38), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.006 0.001 HIS H 35 PHE 0.010 0.001 PHE H 27 TYR 0.009 0.001 TYR A 453 ARG 0.004 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00215 ( 1) link_NAG-ASN : angle 1.04802 ( 3) hydrogen bonds : bond 0.02774 ( 102) hydrogen bonds : angle 6.35291 ( 255) SS BOND : bond 0.00267 ( 5) SS BOND : angle 0.82252 ( 10) covalent geometry : bond 0.00310 ( 3496) covalent geometry : angle 0.56668 ( 4749) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.373 Fit side-chains REVERT: A 365 TYR cc_start: 0.7966 (m-80) cc_final: 0.7722 (m-80) REVERT: A 468 ILE cc_start: 0.9136 (pt) cc_final: 0.8786 (mt) REVERT: L 61 ARG cc_start: 0.7257 (ptt180) cc_final: 0.6929 (ptp-170) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 0.1896 time to fit residues: 19.6880 Evaluate side-chains 82 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.5980 chunk 35 optimal weight: 0.7980 chunk 7 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.4980 chunk 14 optimal weight: 0.0370 chunk 13 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 64 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.169399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.143435 restraints weight = 4343.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.147555 restraints weight = 2637.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.150320 restraints weight = 1902.208| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3502 Z= 0.150 Angle : 0.606 9.193 4762 Z= 0.295 Chirality : 0.042 0.144 505 Planarity : 0.005 0.092 620 Dihedral : 4.695 23.754 505 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 4.63 % Allowed : 19.89 % Favored : 75.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.42), residues: 431 helix: -1.17 (1.05), residues: 28 sheet: 0.42 (0.48), residues: 129 loop : -0.62 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.010 0.001 PHE H 27 TYR 0.009 0.001 TYR A 453 ARG 0.005 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00187 ( 1) link_NAG-ASN : angle 1.13221 ( 3) hydrogen bonds : bond 0.02816 ( 102) hydrogen bonds : angle 6.32483 ( 255) SS BOND : bond 0.00299 ( 5) SS BOND : angle 0.88262 ( 10) covalent geometry : bond 0.00360 ( 3496) covalent geometry : angle 0.60454 ( 4749) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.358 Fit side-chains REVERT: A 365 TYR cc_start: 0.7984 (m-80) cc_final: 0.7754 (m-80) REVERT: A 468 ILE cc_start: 0.9135 (pt) cc_final: 0.8768 (mt) outliers start: 17 outliers final: 14 residues processed: 87 average time/residue: 0.1848 time to fit residues: 19.2755 Evaluate side-chains 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 107 THR Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 79 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 30 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 39 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 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 = 0.4026 r_free = 0.4026 target = 0.166774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.141038 restraints weight = 4216.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.145069 restraints weight = 2617.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.147699 restraints weight = 1915.242| |-----------------------------------------------------------------------------| r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3502 Z= 0.160 Angle : 0.603 9.928 4762 Z= 0.296 Chirality : 0.042 0.145 505 Planarity : 0.005 0.090 620 Dihedral : 4.722 23.090 505 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.81 % Allowed : 20.16 % Favored : 76.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.42), residues: 431 helix: -1.17 (1.05), residues: 28 sheet: 0.40 (0.47), residues: 129 loop : -0.57 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.010 0.001 PHE H 27 TYR 0.010 0.001 TYR L 91 ARG 0.004 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00167 ( 1) link_NAG-ASN : angle 1.17111 ( 3) hydrogen bonds : bond 0.02814 ( 102) hydrogen bonds : angle 6.31149 ( 255) SS BOND : bond 0.00331 ( 5) SS BOND : angle 0.86617 ( 10) covalent geometry : bond 0.00383 ( 3496) covalent geometry : angle 0.60181 ( 4749) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.352 Fit side-chains REVERT: A 365 TYR cc_start: 0.8023 (m-80) cc_final: 0.7795 (m-80) REVERT: A 468 ILE cc_start: 0.9127 (pt) cc_final: 0.8752 (mt) outliers start: 14 outliers final: 12 residues processed: 88 average time/residue: 0.1740 time to fit residues: 18.2678 Evaluate side-chains 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 0.8980 chunk 12 optimal weight: 0.0970 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 2 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 13 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 GLN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.167561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.143250 restraints weight = 4170.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.146745 restraints weight = 2771.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.148746 restraints weight = 2100.004| |-----------------------------------------------------------------------------| r_work (final): 0.3829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3502 Z= 0.137 Angle : 0.625 9.516 4762 Z= 0.298 Chirality : 0.042 0.142 505 Planarity : 0.005 0.091 620 Dihedral : 4.674 23.799 505 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.09 % Allowed : 20.71 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.42), residues: 431 helix: -1.11 (1.08), residues: 28 sheet: 0.38 (0.47), residues: 131 loop : -0.55 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.007 0.002 HIS H 35 PHE 0.010 0.001 PHE H 27 TYR 0.012 0.001 TYR H 32 ARG 0.005 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00189 ( 1) link_NAG-ASN : angle 1.06560 ( 3) hydrogen bonds : bond 0.02651 ( 102) hydrogen bonds : angle 6.25376 ( 255) SS BOND : bond 0.00297 ( 5) SS BOND : angle 0.73713 ( 10) covalent geometry : bond 0.00329 ( 3496) covalent geometry : angle 0.62441 ( 4749) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.341 Fit side-chains REVERT: A 365 TYR cc_start: 0.7911 (m-80) cc_final: 0.7697 (m-80) REVERT: A 468 ILE cc_start: 0.9130 (pt) cc_final: 0.8787 (mt) REVERT: H 72 ASP cc_start: 0.7774 (t0) cc_final: 0.6930 (t0) REVERT: H 75 LYS cc_start: 0.8761 (mmmt) cc_final: 0.8447 (mtpt) REVERT: H 108 MET cc_start: 0.8109 (tpt) cc_final: 0.7626 (tpt) outliers start: 15 outliers final: 13 residues processed: 86 average time/residue: 0.1742 time to fit residues: 17.8915 Evaluate side-chains 84 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 TYR Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 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 = 0.3795 r_free = 0.3795 target = 0.151239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.125670 restraints weight = 4468.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.129392 restraints weight = 2725.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131828 restraints weight = 1978.699| |-----------------------------------------------------------------------------| r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.3527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3502 Z= 0.194 Angle : 0.649 10.210 4762 Z= 0.317 Chirality : 0.043 0.148 505 Planarity : 0.006 0.093 620 Dihedral : 4.893 23.426 505 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 11.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 3.54 % Allowed : 20.71 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.54 (0.42), residues: 431 helix: -1.17 (1.07), residues: 28 sheet: 0.32 (0.47), residues: 131 loop : -0.59 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.007 0.002 HIS H 35 PHE 0.011 0.001 PHE H 27 TYR 0.013 0.001 TYR H 32 ARG 0.003 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00130 ( 1) link_NAG-ASN : angle 1.33151 ( 3) hydrogen bonds : bond 0.02914 ( 102) hydrogen bonds : angle 6.35287 ( 255) SS BOND : bond 0.00399 ( 5) SS BOND : angle 0.93079 ( 10) covalent geometry : bond 0.00460 ( 3496) covalent geometry : angle 0.64737 ( 4749) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.366 Fit side-chains REVERT: A 365 TYR cc_start: 0.8048 (m-80) cc_final: 0.7821 (m-80) REVERT: A 468 ILE cc_start: 0.9141 (pt) cc_final: 0.8746 (mt) outliers start: 13 outliers final: 12 residues processed: 87 average time/residue: 0.1928 time to fit residues: 19.7275 Evaluate side-chains 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 20 optimal weight: 0.0870 chunk 26 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.153396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127890 restraints weight = 4507.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.131634 restraints weight = 2731.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134139 restraints weight = 1968.624| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.3628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3502 Z= 0.146 Angle : 0.645 10.007 4762 Z= 0.306 Chirality : 0.042 0.143 505 Planarity : 0.006 0.090 620 Dihedral : 4.743 23.674 505 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.81 % Allowed : 20.98 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.42), residues: 431 helix: -1.00 (1.10), residues: 28 sheet: 0.41 (0.47), residues: 129 loop : -0.58 (0.39), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.008 0.002 HIS H 35 PHE 0.009 0.001 PHE H 27 TYR 0.010 0.001 TYR H 32 ARG 0.004 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00180 ( 1) link_NAG-ASN : angle 1.13574 ( 3) hydrogen bonds : bond 0.02730 ( 102) hydrogen bonds : angle 6.25625 ( 255) SS BOND : bond 0.00314 ( 5) SS BOND : angle 0.78475 ( 10) covalent geometry : bond 0.00355 ( 3496) covalent geometry : angle 0.64380 ( 4749) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 862 Ramachandran restraints generated. 431 Oldfield, 0 Emsley, 431 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.379 Fit side-chains REVERT: A 365 TYR cc_start: 0.8038 (m-80) cc_final: 0.7780 (m-80) REVERT: A 468 ILE cc_start: 0.9137 (pt) cc_final: 0.8779 (mt) outliers start: 14 outliers final: 13 residues processed: 86 average time/residue: 0.1718 time to fit residues: 17.7664 Evaluate side-chains 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 92 CYS Chi-restraints excluded: chain H residue 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 13 VAL Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 38 GLN Chi-restraints excluded: chain L residue 85 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 5 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 38 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 = 0.3806 r_free = 0.3806 target = 0.151788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.126458 restraints weight = 4485.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.130031 restraints weight = 2714.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132505 restraints weight = 1971.715| |-----------------------------------------------------------------------------| r_work (final): 0.3588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3502 Z= 0.187 Angle : 0.657 10.307 4762 Z= 0.317 Chirality : 0.043 0.145 505 Planarity : 0.006 0.093 620 Dihedral : 4.849 23.740 505 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 3.27 % Allowed : 21.53 % Favored : 75.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.42), residues: 431 helix: -1.12 (1.08), residues: 28 sheet: 0.20 (0.47), residues: 131 loop : -0.59 (0.40), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.007 0.002 HIS H 35 PHE 0.009 0.001 PHE H 27 TYR 0.017 0.001 TYR H 32 ARG 0.004 0.000 ARG A 346 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 1) link_NAG-ASN : angle 1.28648 ( 3) hydrogen bonds : bond 0.02874 ( 102) hydrogen bonds : angle 6.33486 ( 255) SS BOND : bond 0.00382 ( 5) SS BOND : angle 0.86850 ( 10) covalent geometry : bond 0.00447 ( 3496) covalent geometry : angle 0.65581 ( 4749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1710.65 seconds wall clock time: 30 minutes 27.69 seconds (1827.69 seconds total)