Starting phenix.real_space_refine on Wed Jun 4 16:29:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i3u_35156/06_2025/8i3u_35156.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i3u_35156/06_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_35156/06_2025/8i3u_35156.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i3u_35156/06_2025/8i3u_35156.map" model { file = "/net/cci-nas-00/data/ceres_data/8i3u_35156/06_2025/8i3u_35156.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i3u_35156/06_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-5710/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: 3.65, per 1000 atoms: 1.07 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: 0.75 Conformation dependent library (CDL) restraints added in 384.7 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: 0.39 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: 0.89 Time building geometry restraints manager: 0.92 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: 4.500 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.830 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.590 ------------------------------------------------------------------------------- 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 : 0.361 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: 0.1936 time to fit residues: 26.2329 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 : 0.390 ------------------------------------------------------------------------------- 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: 0.1980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.156534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.131186 restraints weight = 4357.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.135044 restraints weight = 2687.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137370 restraints weight = 1949.374| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3502 Z= 0.184 Angle : 0.603 8.427 4762 Z= 0.309 Chirality : 0.043 0.153 505 Planarity : 0.006 0.091 620 Dihedral : 4.994 26.166 505 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 3.54 % Allowed : 14.44 % Favored : 82.02 % 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: -0.55 (0.41), residues: 431 helix: -1.40 (0.99), residues: 28 sheet: 0.13 (0.48), residues: 124 loop : -0.44 (0.38), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.001 PHE A 342 TYR 0.018 0.002 TYR L 91 ARG 0.005 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00188 ( 1) link_NAG-ASN : angle 0.99938 ( 3) hydrogen bonds : bond 0.03695 ( 102) hydrogen bonds : angle 6.97142 ( 255) SS BOND : bond 0.00381 ( 5) SS BOND : angle 1.04204 ( 10) covalent geometry : bond 0.00437 ( 3496) covalent geometry : angle 0.60178 ( 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 : 0.418 Fit side-chains REVERT: A 365 TYR cc_start: 0.7990 (m-80) cc_final: 0.7732 (m-80) outliers start: 13 outliers final: 10 residues processed: 97 average time/residue: 0.1876 time to fit residues: 21.5694 Evaluate side-chains 91 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 1.9990 chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.165090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139646 restraints weight = 4140.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.143669 restraints weight = 2577.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.146322 restraints weight = 1882.655| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.2871 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 : 0.608 8.830 4762 Z= 0.306 Chirality : 0.043 0.148 505 Planarity : 0.005 0.086 620 Dihedral : 4.909 21.921 505 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 4.36 % Allowed : 16.08 % Favored : 79.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.60 (0.41), residues: 431 helix: -1.43 (0.98), residues: 28 sheet: 0.12 (0.47), residues: 132 loop : -0.51 (0.39), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.005 0.001 HIS H 35 PHE 0.012 0.001 PHE H 27 TYR 0.017 0.001 TYR L 91 ARG 0.003 0.000 ARG A 457 Details of bonding type rmsd link_NAG-ASN : bond 0.00149 ( 1) link_NAG-ASN : angle 1.23335 ( 3) hydrogen bonds : bond 0.03242 ( 102) hydrogen bonds : angle 6.78402 ( 255) SS BOND : bond 0.00367 ( 5) SS BOND : angle 1.30030 ( 10) covalent geometry : bond 0.00445 ( 3496) covalent geometry : angle 0.60520 ( 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: 16 poor density : 81 time to evaluate : 0.385 Fit side-chains REVERT: A 365 TYR cc_start: 0.7982 (m-80) cc_final: 0.7746 (m-80) outliers start: 16 outliers final: 12 residues processed: 90 average time/residue: 0.2106 time to fit residues: 22.0665 Evaluate side-chains 91 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 100 VAL Chi-restraints excluded: chain H residue 110 THR Chi-restraints excluded: chain L residue 2 ILE 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: 0.7980 chunk 12 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 41 optimal weight: 0.4980 chunk 24 optimal weight: 0.0070 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 overall best weight: 0.4198 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.161961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.137088 restraints weight = 4480.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.141067 restraints weight = 2708.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.143696 restraints weight = 1936.976| |-----------------------------------------------------------------------------| r_work (final): 0.3728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7646 moved from start: 0.3058 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= 0.135 Angle : 0.588 8.752 4762 Z= 0.287 Chirality : 0.042 0.143 505 Planarity : 0.005 0.089 620 Dihedral : 4.693 24.094 505 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.54 % Allowed : 17.17 % Favored : 79.29 % 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: -0.53 (0.41), residues: 431 helix: -1.37 (0.99), residues: 28 sheet: 0.35 (0.47), residues: 129 loop : -0.57 (0.39), 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 0.011 0.001 PHE H 27 TYR 0.010 0.001 TYR L 91 ARG 0.005 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00203 ( 1) link_NAG-ASN : angle 1.01728 ( 3) hydrogen bonds : bond 0.02907 ( 102) hydrogen bonds : angle 6.45731 ( 255) SS BOND : bond 0.00271 ( 5) SS BOND : angle 0.94612 ( 10) covalent geometry : bond 0.00322 ( 3496) covalent geometry : angle 0.58654 ( 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 96 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.328 Fit side-chains REVERT: A 468 ILE cc_start: 0.9170 (pt) cc_final: 0.8855 (mt) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.1975 time to fit residues: 21.3109 Evaluate side-chains 87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 110 THR 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: 1.9990 chunk 17 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 34 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.1980 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 27 optimal weight: 0.0060 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 GLN H 64 GLN L 38 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.158682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.133526 restraints weight = 4398.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137401 restraints weight = 2684.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.139991 restraints weight = 1944.616| |-----------------------------------------------------------------------------| r_work (final): 0.3714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3227 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= 0.144 Angle : 0.587 10.167 4762 Z= 0.284 Chirality : 0.042 0.145 505 Planarity : 0.005 0.089 620 Dihedral : 4.675 22.991 505 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.54 % Allowed : 21.53 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.58 (0.42), residues: 431 helix: -1.35 (1.00), residues: 28 sheet: 0.13 (0.47), residues: 135 loop : -0.51 (0.39), residues: 268 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 0.011 0.001 PHE H 27 TYR 0.010 0.001 TYR A 453 ARG 0.004 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00185 ( 1) link_NAG-ASN : angle 1.10825 ( 3) hydrogen bonds : bond 0.02842 ( 102) hydrogen bonds : angle 6.32210 ( 255) SS BOND : bond 0.00285 ( 5) SS BOND : angle 0.88752 ( 10) covalent geometry : bond 0.00343 ( 3496) covalent geometry : angle 0.58571 ( 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 91 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 78 time to evaluate : 0.616 Fit side-chains REVERT: A 468 ILE cc_start: 0.9153 (pt) cc_final: 0.8861 (mt) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 0.1815 time to fit residues: 18.7312 Evaluate side-chains 87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.353 ------------------------------------------------------------------------------- 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 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 110 THR Chi-restraints excluded: chain L residue 38 GLN 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: 2.9990 chunk 35 optimal weight: 0.6980 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.131299 restraints weight = 4529.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.135207 restraints weight = 2750.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.137806 restraints weight = 1990.636| |-----------------------------------------------------------------------------| r_work (final): 0.3684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3502 Z= 0.201 Angle : 0.640 10.018 4762 Z= 0.312 Chirality : 0.043 0.148 505 Planarity : 0.006 0.094 620 Dihedral : 4.900 24.000 505 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 4.63 % Allowed : 20.44 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.62 (0.41), residues: 431 helix: -1.30 (1.03), residues: 28 sheet: 0.33 (0.47), residues: 128 loop : -0.67 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 47 HIS 0.007 0.002 HIS H 35 PHE 0.011 0.001 PHE H 27 TYR 0.012 0.002 TYR L 91 ARG 0.004 0.001 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00122 ( 1) link_NAG-ASN : angle 1.32233 ( 3) hydrogen bonds : bond 0.02981 ( 102) hydrogen bonds : angle 6.41079 ( 255) SS BOND : bond 0.00379 ( 5) SS BOND : angle 0.96850 ( 10) covalent geometry : bond 0.00476 ( 3496) covalent geometry : angle 0.63838 ( 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 94 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 77 time to evaluate : 0.352 Fit side-chains REVERT: A 468 ILE cc_start: 0.9164 (pt) cc_final: 0.8850 (mt) REVERT: H 76 ASN cc_start: 0.8924 (OUTLIER) cc_final: 0.8688 (m-40) outliers start: 17 outliers final: 14 residues processed: 89 average time/residue: 0.1736 time to fit residues: 18.3943 Evaluate side-chains 87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.352 ------------------------------------------------------------------------------- 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 459 SER Chi-restraints excluded: chain A residue 466 ARG Chi-restraints excluded: chain H residue 5 VAL Chi-restraints excluded: chain H residue 76 ASN 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 33 LEU Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.151902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.127586 restraints weight = 4541.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.131107 restraints weight = 2754.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.133547 restraints weight = 1991.867| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3486 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= 0.170 Angle : 0.623 10.110 4762 Z= 0.304 Chirality : 0.042 0.146 505 Planarity : 0.006 0.089 620 Dihedral : 4.844 23.054 505 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % 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: -0.62 (0.41), residues: 431 helix: -1.26 (1.05), residues: 28 sheet: 0.32 (0.47), residues: 128 loop : -0.67 (0.39), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.007 0.002 HIS H 35 PHE 0.011 0.001 PHE H 27 TYR 0.012 0.001 TYR L 91 ARG 0.004 0.001 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00154 ( 1) link_NAG-ASN : angle 1.21672 ( 3) hydrogen bonds : bond 0.02864 ( 102) hydrogen bonds : angle 6.36658 ( 255) SS BOND : bond 0.00351 ( 5) SS BOND : angle 0.87928 ( 10) covalent geometry : bond 0.00406 ( 3496) covalent geometry : angle 0.62196 ( 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 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.325 Fit side-chains REVERT: A 468 ILE cc_start: 0.9154 (pt) cc_final: 0.8854 (mt) REVERT: L 61 ARG cc_start: 0.7312 (ptp-170) cc_final: 0.6880 (ptp-170) outliers start: 15 outliers final: 13 residues processed: 83 average time/residue: 0.1766 time to fit residues: 17.4948 Evaluate side-chains 83 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 70 time to evaluate : 0.387 ------------------------------------------------------------------------------- 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 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 33 LEU Chi-restraints excluded: chain L residue 38 GLN 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: 0.6980 chunk 23 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 29 optimal weight: 0.0770 chunk 32 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 41 optimal weight: 0.1980 chunk 13 optimal weight: 0.9990 chunk 5 optimal weight: 0.0570 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.152745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.127300 restraints weight = 4472.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.131049 restraints weight = 2721.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.133533 restraints weight = 1963.229| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.3537 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= 0.123 Angle : 0.610 9.364 4762 Z= 0.293 Chirality : 0.042 0.139 505 Planarity : 0.005 0.089 620 Dihedral : 4.618 24.052 505 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 3.54 % Allowed : 21.80 % Favored : 74.66 % 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: -1.10 (1.09), residues: 28 sheet: 0.36 (0.47), residues: 129 loop : -0.58 (0.39), residues: 274 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 0.009 0.001 PHE H 27 TYR 0.009 0.001 TYR H 32 ARG 0.005 0.000 ARG H 100J Details of bonding type rmsd link_NAG-ASN : bond 0.00209 ( 1) link_NAG-ASN : angle 0.98828 ( 3) hydrogen bonds : bond 0.02620 ( 102) hydrogen bonds : angle 6.23754 ( 255) SS BOND : bond 0.00249 ( 5) SS BOND : angle 0.68903 ( 10) covalent geometry : bond 0.00298 ( 3496) covalent geometry : angle 0.60912 ( 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 87 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 0.414 Fit side-chains REVERT: A 468 ILE cc_start: 0.9155 (pt) cc_final: 0.8901 (mt) outliers start: 13 outliers final: 11 residues processed: 83 average time/residue: 0.1849 time to fit residues: 18.4142 Evaluate side-chains 81 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.383 ------------------------------------------------------------------------------- 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 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 33 LEU Chi-restraints excluded: chain L residue 38 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 76 ASN L 38 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.151253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.126973 restraints weight = 4468.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130476 restraints weight = 2734.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.132646 restraints weight = 1984.320| |-----------------------------------------------------------------------------| r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3502 Z= 0.223 Angle : 0.666 10.316 4762 Z= 0.329 Chirality : 0.043 0.150 505 Planarity : 0.006 0.093 620 Dihedral : 5.003 23.628 505 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.36 % Allowed : 21.53 % Favored : 74.11 % 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: -0.72 (0.41), residues: 431 helix: -1.25 (1.05), residues: 28 sheet: 0.02 (0.48), residues: 117 loop : -0.60 (0.38), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 47 HIS 0.007 0.002 HIS H 35 PHE 0.011 0.001 PHE H 27 TYR 0.011 0.002 TYR A 453 ARG 0.005 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00114 ( 1) link_NAG-ASN : angle 1.44112 ( 3) hydrogen bonds : bond 0.02992 ( 102) hydrogen bonds : angle 6.42464 ( 255) SS BOND : bond 0.00414 ( 5) SS BOND : angle 0.96143 ( 10) covalent geometry : bond 0.00525 ( 3496) covalent geometry : angle 0.66449 ( 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 90 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 0.360 Fit side-chains REVERT: A 468 ILE cc_start: 0.9158 (pt) cc_final: 0.8848 (mt) REVERT: L 6 GLN cc_start: 0.7082 (mt0) cc_final: 0.6690 (tt0) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.1961 time to fit residues: 19.8055 Evaluate side-chains 84 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 29 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 36 optimal weight: 0.1980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 38 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.152773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.128295 restraints weight = 4545.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.131876 restraints weight = 2763.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.134334 restraints weight = 1999.480| |-----------------------------------------------------------------------------| r_work (final): 0.3594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.3737 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= 0.163 Angle : 0.659 10.298 4762 Z= 0.319 Chirality : 0.043 0.146 505 Planarity : 0.006 0.090 620 Dihedral : 4.819 23.557 505 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 3.81 % Allowed : 22.07 % Favored : 74.11 % 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: -1.12 (1.08), residues: 28 sheet: 0.30 (0.47), residues: 129 loop : -0.58 (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 0.013 0.001 TYR H 32 ARG 0.005 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00146 ( 1) link_NAG-ASN : angle 1.21929 ( 3) hydrogen bonds : bond 0.02789 ( 102) hydrogen bonds : angle 6.44240 ( 255) SS BOND : bond 0.00358 ( 5) SS BOND : angle 1.40852 ( 10) covalent geometry : bond 0.00391 ( 3496) covalent geometry : angle 0.65561 ( 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 89 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 75 time to evaluate : 0.406 Fit side-chains REVERT: A 468 ILE cc_start: 0.9151 (pt) cc_final: 0.8885 (mt) REVERT: L 6 GLN cc_start: 0.6826 (mt0) cc_final: 0.6532 (tt0) outliers start: 14 outliers final: 12 residues processed: 84 average time/residue: 0.2027 time to fit residues: 20.1043 Evaluate side-chains 84 residues out of total 367 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.151407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.126655 restraints weight = 4520.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.130191 restraints weight = 2792.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132526 restraints weight = 2032.663| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3502 Z= 0.218 Angle : 0.672 10.685 4762 Z= 0.333 Chirality : 0.043 0.149 505 Planarity : 0.006 0.094 620 Dihedral : 4.995 24.213 505 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.27 % Allowed : 21.80 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.71 (0.41), residues: 431 helix: -1.26 (1.04), residues: 28 sheet: 0.08 (0.46), residues: 124 loop : -0.62 (0.39), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP H 47 HIS 0.006 0.002 HIS H 35 PHE 0.011 0.001 PHE H 27 TYR 0.011 0.001 TYR A 453 ARG 0.004 0.001 ARG L 61 Details of bonding type rmsd link_NAG-ASN : bond 0.00126 ( 1) link_NAG-ASN : angle 1.44916 ( 3) hydrogen bonds : bond 0.02958 ( 102) hydrogen bonds : angle 6.52398 ( 255) SS BOND : bond 0.00413 ( 5) SS BOND : angle 1.47733 ( 10) covalent geometry : bond 0.00519 ( 3496) covalent geometry : angle 0.66873 ( 4749) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1827.23 seconds wall clock time: 32 minutes 7.57 seconds (1927.57 seconds total)