Starting phenix.real_space_refine on Wed Jul 1 22:00:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7tas_25783/07_2026/7tas_25783.cif Found real_map, /net/cci-nas-00/data/ceres_data/7tas_25783/07_2026/7tas_25783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7tas_25783/07_2026/7tas_25783.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7tas_25783/07_2026/7tas_25783.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7tas_25783/07_2026/7tas_25783.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7tas_25783/07_2026/7tas_25783.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7tas_25783/07_2026/7tas_25783.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7tas_25783/07_2026/7tas_25783.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.054 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 14 5.16 5 C 2014 2.51 5 N 549 2.21 5 O 570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 3147 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 904 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 17 Chain: "L" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 751 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1454 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 54 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.97, per 1000 atoms: 0.31 Number of scatterers: 3147 At special positions: 0 Unit cell: (61, 82, 81, 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 14 16.00 O 570 8.00 N 549 7.00 C 2014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.05 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.15 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.23 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.17 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " BETA1-6 " NAG A 1 " - " FUC A 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN E 343 " Time building additional restraints: 0.29 Conformation dependent library (CDL) restraints added in 117.6 milliseconds 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 10.6% alpha, 30.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 80 through 84 removed outlier: 3.815A pdb=" N GLU L 84 " --> pdb=" O SER L 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.877A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.559A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 removed outlier: 3.504A pdb=" N TYR E 421 " --> pdb=" O LYS E 417 " (cutoff:3.500A) Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.563A pdb=" N HIS H 59 " --> pdb=" O LEU H 50 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N MET H 34 " --> pdb=" O LEU H 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.550A pdb=" N ALA L 10 " --> pdb=" O THR L 107 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.550A pdb=" N ALA L 10 " --> pdb=" O THR L 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA6, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.531A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.699A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'E' and resid 473 through 474 100 hydrogen bonds defined for protein. 234 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: 0.47 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 911 1.33 - 1.47: 920 1.47 - 1.60: 1382 1.60 - 1.73: 0 1.73 - 1.86: 16 Bond restraints: 3229 Sorted by residual: bond pdb=" N CYS E 391 " pdb=" CA CYS E 391 " ideal model delta sigma weight residual 1.454 1.534 -0.080 1.23e-02 6.61e+03 4.27e+01 bond pdb=" C CYS E 336 " pdb=" O CYS E 336 " ideal model delta sigma weight residual 1.237 1.313 -0.076 1.29e-02 6.01e+03 3.47e+01 bond pdb=" CA ILE L 29 " pdb=" CB ILE L 29 " ideal model delta sigma weight residual 1.544 1.493 0.051 1.17e-02 7.31e+03 1.90e+01 bond pdb=" N CYS E 336 " pdb=" CA CYS E 336 " ideal model delta sigma weight residual 1.454 1.401 0.053 1.29e-02 6.01e+03 1.70e+01 bond pdb=" CA SER L 95 " pdb=" C SER L 95 " ideal model delta sigma weight residual 1.524 1.480 0.044 1.26e-02 6.30e+03 1.20e+01 ... (remaining 3224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 3524 1.69 - 3.37: 709 3.37 - 5.06: 116 5.06 - 6.74: 40 6.74 - 8.43: 12 Bond angle restraints: 4401 Sorted by residual: angle pdb=" C GLN L 6 " pdb=" N PRO L 7 " pdb=" CA PRO L 7 " ideal model delta sigma weight residual 119.66 125.93 -6.27 7.30e-01 1.88e+00 7.38e+01 angle pdb=" C THR E 478 " pdb=" N PRO E 479 " pdb=" CA PRO E 479 " ideal model delta sigma weight residual 119.90 128.33 -8.43 1.05e+00 9.07e-01 6.44e+01 angle pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta sigma weight residual 119.87 127.54 -7.67 1.04e+00 9.25e-01 5.44e+01 angle pdb=" C VAL L 59 " pdb=" N PRO L 60 " pdb=" CA PRO L 60 " ideal model delta sigma weight residual 120.03 127.01 -6.98 9.90e-01 1.02e+00 4.97e+01 angle pdb=" C ARG L 55 " pdb=" N PRO L 56 " pdb=" CA PRO L 56 " ideal model delta sigma weight residual 120.31 127.17 -6.86 9.80e-01 1.04e+00 4.89e+01 ... (remaining 4396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.95: 1717 15.95 - 31.90: 98 31.90 - 47.84: 20 47.84 - 63.79: 7 63.79 - 79.74: 4 Dihedral angle restraints: 1846 sinusoidal: 661 harmonic: 1185 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 49.70 43.30 1 1.00e+01 1.00e-02 2.61e+01 dihedral pdb=" CA SER H 109 " pdb=" C SER H 109 " pdb=" N ASP H 110 " pdb=" CA ASP H 110 " ideal model delta harmonic sigma weight residual -180.00 -160.42 -19.58 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" N LYS L 97 " pdb=" C LYS L 97 " pdb=" CA LYS L 97 " pdb=" CB LYS L 97 " ideal model delta harmonic sigma weight residual 122.80 132.21 -9.41 0 2.50e+00 1.60e-01 1.42e+01 ... (remaining 1843 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 354 0.092 - 0.183: 111 0.183 - 0.275: 14 0.275 - 0.367: 2 0.367 - 0.458: 2 Chirality restraints: 483 Sorted by residual: chirality pdb=" C1 FUC A 3 " pdb=" O6 NAG A 1 " pdb=" C2 FUC A 3 " pdb=" O5 FUC A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-02 2.50e+03 1.23e+02 chirality pdb=" CA CYS E 336 " pdb=" N CYS E 336 " pdb=" C CYS E 336 " pdb=" CB CYS E 336 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.25e+00 chirality pdb=" CA CYS E 391 " pdb=" N CYS E 391 " pdb=" C CYS E 391 " pdb=" CB CYS E 391 " both_signs ideal model delta sigma weight residual False 2.51 2.88 -0.37 2.00e-01 2.50e+01 3.43e+00 ... (remaining 480 not shown) Planarity restraints: 569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " 0.207 2.00e-02 2.50e+03 1.75e-01 3.82e+02 pdb=" C7 NAG A 2 " -0.045 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.042 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " -0.283 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.162 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.141 2.00e-02 2.50e+03 1.16e-01 1.69e+02 pdb=" C7 NAG A 1 " -0.038 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " 0.105 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.187 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS H 22 " -0.024 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C CYS H 22 " 0.086 2.00e-02 2.50e+03 pdb=" O CYS H 22 " -0.034 2.00e-02 2.50e+03 pdb=" N ALA H 23 " -0.028 2.00e-02 2.50e+03 ... (remaining 566 not shown) Histogram of nonbonded interaction distances: 2.45 - 2.94: 1424 2.94 - 3.43: 2587 3.43 - 3.92: 5073 3.92 - 4.41: 5879 4.41 - 4.90: 9789 Nonbonded interactions: 24752 Sorted by model distance: nonbonded pdb=" O ASP L 93 " pdb=" O LEU L 96 " model vdw 2.452 3.040 nonbonded pdb=" O SER L 68 " pdb=" OG SER L 68 " model vdw 2.453 3.040 nonbonded pdb=" O ILE L 29 " pdb=" C GLY L 30 " model vdw 2.540 3.270 nonbonded pdb=" C ASP E 364 " pdb=" OD1 ASP E 364 " model vdw 2.569 3.270 nonbonded pdb=" OD1 ASP E 364 " pdb=" N SER E 366 " model vdw 2.580 3.120 ... (remaining 24747 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.570 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 4.990 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 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 : 0.014 0.202 3238 Z= 0.822 Angle : 1.534 11.801 4422 Z= 1.034 Chirality : 0.089 0.458 483 Planarity : 0.011 0.175 568 Dihedral : 11.504 79.738 1080 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.69 % Allowed : 3.04 % Favored : 95.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.01 (0.38), residues: 409 helix: -5.04 (0.23), residues: 32 sheet: 0.13 (0.41), residues: 139 loop : -0.45 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 72 TYR 0.033 0.005 TYR H 95 PHE 0.020 0.003 PHE E 497 TRP 0.026 0.005 TRP H 47 HIS 0.006 0.002 HIS H 32 Details of bonding type rmsd/Z covalent geometry : bond 0.01312 / 0.79 ( 3229) covalent geometry : angle 1.49718 / 1.02 ( 4401) SS BOND : bond 0.11198 / 5.85 ( 6) SS BOND : angle 5.81368 / 3.23 ( 12) hydrogen bonds : bond 0.22761 / 15.58 ( 98) hydrogen bonds : angle 10.56425 / 7.30 ( 234) link_BETA1-4 : bond 0.00600 / 0.32 ( 1) link_BETA1-4 : angle 3.11300 / 1.63 ( 3) link_BETA1-6 : bond 0.00453 / 0.24 ( 1) link_BETA1-6 : angle 1.02500 / 0.56 ( 3) link_NAG-ASN : bond 0.00932 / 0.49 ( 1) link_NAG-ASN : angle 5.93348 / 3.42 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 65 time to evaluate : 0.136 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 70 average time/residue: 0.1044 time to fit residues: 8.3468 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 368 LEU Chi-restraints excluded: chain E residue 392 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 32 HIS H 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.100357 restraints weight = 4826.290| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.85 r_work: 0.3112 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3238 Z= 0.155 Angle : 0.669 9.079 4422 Z= 0.339 Chirality : 0.045 0.144 483 Planarity : 0.004 0.035 568 Dihedral : 4.813 29.911 459 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.24 % Allowed : 1.71 % Favored : 98.04 % Rotamer: Outliers : 1.69 % Allowed : 9.80 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.40), residues: 409 helix: -4.22 (0.68), residues: 26 sheet: 0.29 (0.40), residues: 139 loop : 0.09 (0.39), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 457 TYR 0.013 0.002 TYR H 60 PHE 0.013 0.002 PHE E 377 TRP 0.015 0.002 TRP E 353 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 3229) covalent geometry : angle 0.64366 / 0.33 ( 4401) SS BOND : bond 0.00250 / 0.13 ( 6) SS BOND : angle 1.23617 / 0.61 ( 12) hydrogen bonds : bond 0.03881 / 2.76 ( 98) hydrogen bonds : angle 7.50472 / 5.13 ( 234) link_BETA1-4 : bond 0.00049 / 0.03 ( 1) link_BETA1-4 : angle 5.16604 / 2.71 ( 3) link_BETA1-6 : bond 0.01027 / 0.54 ( 1) link_BETA1-6 : angle 1.67514 / 0.85 ( 3) link_NAG-ASN : bond 0.00114 / 0.06 ( 1) link_NAG-ASN : angle 3.94300 / 2.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.120 Fit side-chains REVERT: L 47 LEU cc_start: 0.9089 (tp) cc_final: 0.8866 (tp) outliers start: 5 outliers final: 3 residues processed: 61 average time/residue: 0.1038 time to fit residues: 7.2581 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 108 VAL Chi-restraints excluded: chain E residue 461 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 0.0170 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 0.0070 chunk 33 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 24 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.3636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN L 16 GLN E 409 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.107432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.099660 restraints weight = 4849.898| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 1.89 r_work: 0.3095 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 3238 Z= 0.110 Angle : 0.581 8.930 4422 Z= 0.287 Chirality : 0.043 0.150 483 Planarity : 0.003 0.031 568 Dihedral : 4.073 22.206 455 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.03 % Allowed : 10.81 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.41), residues: 409 helix: -3.75 (0.64), residues: 32 sheet: 0.48 (0.41), residues: 139 loop : 0.36 (0.41), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 457 TYR 0.010 0.001 TYR E 453 PHE 0.014 0.001 PHE E 490 TRP 0.009 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.11 ( 3229) covalent geometry : angle 0.55576 / 0.28 ( 4401) SS BOND : bond 0.00223 / 0.11 ( 6) SS BOND : angle 1.05205 / 0.53 ( 12) hydrogen bonds : bond 0.03462 / 2.46 ( 98) hydrogen bonds : angle 6.77692 / 4.66 ( 234) link_BETA1-4 : bond 0.00108 / 0.06 ( 1) link_BETA1-4 : angle 5.34585 / 2.80 ( 3) link_BETA1-6 : bond 0.00917 / 0.48 ( 1) link_BETA1-6 : angle 1.43437 / 0.76 ( 3) link_NAG-ASN : bond 0.00384 / 0.20 ( 1) link_NAG-ASN : angle 3.15979 / 1.81 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.117 Fit side-chains REVERT: H 34 MET cc_start: 0.8975 (mmm) cc_final: 0.8749 (mmm) REVERT: L 47 LEU cc_start: 0.9068 (tp) cc_final: 0.8841 (tp) REVERT: L 48 LEU cc_start: 0.9162 (mt) cc_final: 0.8950 (mt) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.1069 time to fit residues: 7.3380 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN L 16 GLN L 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.102421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.094689 restraints weight = 4850.816| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.91 r_work: 0.3021 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2915 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3238 Z= 0.213 Angle : 0.656 8.799 4422 Z= 0.326 Chirality : 0.046 0.152 483 Planarity : 0.004 0.036 568 Dihedral : 4.251 20.184 455 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.04 % Allowed : 9.80 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.41), residues: 409 helix: -3.63 (0.84), residues: 26 sheet: 0.63 (0.42), residues: 138 loop : 0.08 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG H 102 TYR 0.015 0.002 TYR H 60 PHE 0.012 0.001 PHE E 490 TRP 0.016 0.002 TRP H 47 HIS 0.004 0.002 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00486 / 0.21 ( 3229) covalent geometry : angle 0.62856 / 0.32 ( 4401) SS BOND : bond 0.00305 / 0.15 ( 6) SS BOND : angle 1.31411 / 0.67 ( 12) hydrogen bonds : bond 0.03703 / 2.61 ( 98) hydrogen bonds : angle 6.45381 / 4.39 ( 234) link_BETA1-4 : bond 0.00024 / 0.01 ( 1) link_BETA1-4 : angle 5.31891 / 2.79 ( 3) link_BETA1-6 : bond 0.01060 / 0.56 ( 1) link_BETA1-6 : angle 1.79404 / 0.95 ( 3) link_NAG-ASN : bond 0.00867 / 0.46 ( 1) link_NAG-ASN : angle 4.10419 / 2.37 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.124 Fit side-chains REVERT: L 47 LEU cc_start: 0.9087 (tp) cc_final: 0.8848 (tp) outliers start: 9 outliers final: 7 residues processed: 57 average time/residue: 0.1068 time to fit residues: 7.0452 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 25 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 1 optimal weight: 0.0030 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 16 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.103177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.095573 restraints weight = 4799.689| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.88 r_work: 0.3032 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2927 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3238 Z= 0.152 Angle : 0.611 9.010 4422 Z= 0.296 Chirality : 0.044 0.152 483 Planarity : 0.004 0.036 568 Dihedral : 4.139 20.802 455 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.70 % Allowed : 11.49 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.41), residues: 409 helix: -3.80 (0.74), residues: 26 sheet: 0.68 (0.43), residues: 138 loop : 0.07 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 19 TYR 0.010 0.001 TYR H 60 PHE 0.013 0.001 PHE E 490 TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 ( 3229) covalent geometry : angle 0.58385 / 0.29 ( 4401) SS BOND : bond 0.00244 / 0.12 ( 6) SS BOND : angle 1.13227 / 0.57 ( 12) hydrogen bonds : bond 0.03453 / 2.40 ( 98) hydrogen bonds : angle 6.09926 / 4.19 ( 234) link_BETA1-4 : bond 0.00020 / 0.01 ( 1) link_BETA1-4 : angle 5.39233 / 2.83 ( 3) link_BETA1-6 : bond 0.00829 / 0.44 ( 1) link_BETA1-6 : angle 1.67810 / 0.89 ( 3) link_NAG-ASN : bond 0.00560 / 0.29 ( 1) link_NAG-ASN : angle 3.65099 / 2.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.150 Fit side-chains REVERT: H 102 ARG cc_start: 0.8804 (mtm110) cc_final: 0.8308 (mtm110) outliers start: 8 outliers final: 6 residues processed: 55 average time/residue: 0.1141 time to fit residues: 7.1950 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 13 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 16 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.103286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095895 restraints weight = 4780.771| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.80 r_work: 0.3044 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3238 Z= 0.148 Angle : 0.629 8.885 4422 Z= 0.304 Chirality : 0.045 0.176 483 Planarity : 0.004 0.035 568 Dihedral : 4.157 20.359 455 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.69 % Allowed : 12.50 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.41), residues: 409 helix: -3.89 (0.69), residues: 26 sheet: 0.71 (0.43), residues: 138 loop : 0.06 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 19 TYR 0.010 0.001 TYR H 60 PHE 0.008 0.001 PHE E 490 TRP 0.012 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 ( 3229) covalent geometry : angle 0.60129 / 0.30 ( 4401) SS BOND : bond 0.00839 / 0.49 ( 6) SS BOND : angle 1.45165 / 0.82 ( 12) hydrogen bonds : bond 0.03330 / 2.34 ( 98) hydrogen bonds : angle 5.98860 / 4.12 ( 234) link_BETA1-4 : bond 0.00012 / 0.01 ( 1) link_BETA1-4 : angle 5.32614 / 2.79 ( 3) link_BETA1-6 : bond 0.00897 / 0.47 ( 1) link_BETA1-6 : angle 1.63658 / 0.87 ( 3) link_NAG-ASN : bond 0.00571 / 0.30 ( 1) link_NAG-ASN : angle 3.64235 / 2.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.120 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 54 average time/residue: 0.0972 time to fit residues: 6.0628 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 52 ASN ** 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 = 0.3205 r_free = 0.3205 target = 0.101936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.094420 restraints weight = 4903.995| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.89 r_work: 0.3021 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3238 Z= 0.181 Angle : 0.636 8.857 4422 Z= 0.309 Chirality : 0.045 0.152 483 Planarity : 0.004 0.035 568 Dihedral : 4.220 20.535 455 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.04 % Allowed : 11.15 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.41), residues: 409 helix: -3.93 (0.68), residues: 26 sheet: 0.65 (0.42), residues: 138 loop : -0.02 (0.39), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.013 0.002 TYR H 95 PHE 0.015 0.001 PHE E 490 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.18 ( 3229) covalent geometry : angle 0.60765 / 0.30 ( 4401) SS BOND : bond 0.00480 / 0.27 ( 6) SS BOND : angle 1.31015 / 0.70 ( 12) hydrogen bonds : bond 0.03440 / 2.42 ( 98) hydrogen bonds : angle 5.98271 / 4.12 ( 234) link_BETA1-4 : bond 0.00072 / 0.04 ( 1) link_BETA1-4 : angle 5.34092 / 2.80 ( 3) link_BETA1-6 : bond 0.00909 / 0.48 ( 1) link_BETA1-6 : angle 1.69616 / 0.90 ( 3) link_NAG-ASN : bond 0.00725 / 0.38 ( 1) link_NAG-ASN : angle 3.99539 / 2.30 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 49 time to evaluate : 0.116 Fit side-chains REVERT: H 13 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.6154 (tm-30) REVERT: H 102 ARG cc_start: 0.8767 (mtm110) cc_final: 0.8324 (mtm110) REVERT: L 47 LEU cc_start: 0.9156 (tp) cc_final: 0.8950 (tp) outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 0.0967 time to fit residues: 6.2253 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 382 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.3980 chunk 36 optimal weight: 0.0980 chunk 13 optimal weight: 0.0270 chunk 39 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 52 ASN ** 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 = 0.3234 r_free = 0.3234 target = 0.104277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.096839 restraints weight = 4904.382| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 1.83 r_work: 0.3057 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3238 Z= 0.104 Angle : 0.590 8.948 4422 Z= 0.278 Chirality : 0.043 0.158 483 Planarity : 0.003 0.034 568 Dihedral : 4.040 20.255 455 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.35 % Allowed : 13.18 % Favored : 85.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.41), residues: 409 helix: -3.93 (0.66), residues: 26 sheet: 0.70 (0.43), residues: 138 loop : 0.04 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.009 0.001 TYR E 453 PHE 0.011 0.001 PHE E 490 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.10 ( 3229) covalent geometry : angle 0.56460 / 0.27 ( 4401) SS BOND : bond 0.00295 / 0.16 ( 6) SS BOND : angle 1.08554 / 0.58 ( 12) hydrogen bonds : bond 0.03066 / 2.16 ( 98) hydrogen bonds : angle 5.83017 / 4.02 ( 234) link_BETA1-4 : bond 0.00009 / 0.00 ( 1) link_BETA1-4 : angle 5.33080 / 2.80 ( 3) link_BETA1-6 : bond 0.00876 / 0.46 ( 1) link_BETA1-6 : angle 1.50291 / 0.80 ( 3) link_NAG-ASN : bond 0.00302 / 0.16 ( 1) link_NAG-ASN : angle 3.30058 / 1.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.122 Fit side-chains REVERT: H 102 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8288 (mtm110) REVERT: L 47 LEU cc_start: 0.9120 (tp) cc_final: 0.8895 (tp) outliers start: 4 outliers final: 4 residues processed: 53 average time/residue: 0.1099 time to fit residues: 6.6738 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 0.0060 chunk 17 optimal weight: 0.0030 chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 1 optimal weight: 0.4980 chunk 8 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.2606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.105475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.097997 restraints weight = 4889.801| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.85 r_work: 0.3077 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3238 Z= 0.090 Angle : 0.578 8.825 4422 Z= 0.270 Chirality : 0.042 0.153 483 Planarity : 0.003 0.033 568 Dihedral : 3.897 20.225 455 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.03 % Allowed : 13.51 % Favored : 84.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.41), residues: 409 helix: -3.85 (0.67), residues: 26 sheet: 0.82 (0.43), residues: 138 loop : 0.10 (0.40), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.008 0.001 TYR E 453 PHE 0.010 0.001 PHE E 490 TRP 0.009 0.001 TRP H 47 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00199 / 0.09 ( 3229) covalent geometry : angle 0.55404 / 0.26 ( 4401) SS BOND : bond 0.00181 / 0.09 ( 6) SS BOND : angle 1.05362 / 0.56 ( 12) hydrogen bonds : bond 0.02870 / 2.03 ( 98) hydrogen bonds : angle 5.68380 / 3.92 ( 234) link_BETA1-4 : bond 0.00106 / 0.06 ( 1) link_BETA1-4 : angle 5.17503 / 2.71 ( 3) link_BETA1-6 : bond 0.00900 / 0.47 ( 1) link_BETA1-6 : angle 1.41186 / 0.75 ( 3) link_NAG-ASN : bond 0.00266 / 0.14 ( 1) link_NAG-ASN : angle 3.08179 / 1.76 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.121 Fit side-chains REVERT: H 13 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.6176 (tm-30) REVERT: H 102 ARG cc_start: 0.8769 (mtm110) cc_final: 0.8309 (mtm110) outliers start: 6 outliers final: 5 residues processed: 57 average time/residue: 0.1087 time to fit residues: 7.1276 Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 53 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 6 optimal weight: 0.3980 chunk 38 optimal weight: 0.0470 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.0020 chunk 22 optimal weight: 0.3980 overall best weight: 0.1686 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.107010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.099523 restraints weight = 4771.135| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.84 r_work: 0.3100 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3238 Z= 0.078 Angle : 0.557 8.617 4422 Z= 0.257 Chirality : 0.042 0.151 483 Planarity : 0.003 0.032 568 Dihedral : 3.766 19.427 455 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.03 % Allowed : 14.19 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.41), residues: 409 helix: -3.75 (0.68), residues: 26 sheet: 0.91 (0.43), residues: 138 loop : 0.22 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 19 TYR 0.007 0.001 TYR E 351 PHE 0.010 0.001 PHE E 490 TRP 0.009 0.001 TRP E 436 HIS 0.002 0.000 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00167 / 0.08 ( 3229) covalent geometry : angle 0.53394 / 0.25 ( 4401) SS BOND : bond 0.00162 / 0.09 ( 6) SS BOND : angle 0.90894 / 0.47 ( 12) hydrogen bonds : bond 0.02679 / 1.91 ( 98) hydrogen bonds : angle 5.49120 / 3.78 ( 234) link_BETA1-4 : bond 0.00153 / 0.08 ( 1) link_BETA1-4 : angle 5.13319 / 2.69 ( 3) link_BETA1-6 : bond 0.00795 / 0.42 ( 1) link_BETA1-6 : angle 1.29878 / 0.69 ( 3) link_NAG-ASN : bond 0.00099 / 0.05 ( 1) link_NAG-ASN : angle 2.76158 / 1.58 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 818 Ramachandran restraints generated. 409 Oldfield, 0 Emsley, 409 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.117 Fit side-chains REVERT: H 13 GLN cc_start: 0.6890 (OUTLIER) cc_final: 0.6083 (tm-30) REVERT: H 34 MET cc_start: 0.8897 (mmm) cc_final: 0.8581 (mmm) REVERT: H 102 ARG cc_start: 0.8749 (mtm110) cc_final: 0.8425 (mtm110) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.1072 time to fit residues: 7.1930 Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 13 GLN Chi-restraints excluded: chain L residue 19 THR Chi-restraints excluded: chain E residue 379 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 393 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.9980 chunk 17 optimal weight: 0.0060 chunk 14 optimal weight: 0.0570 chunk 32 optimal weight: 1.9990 chunk 13 optimal weight: 0.0980 chunk 19 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 overall best weight: 0.3314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 6 GLN ** L 52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.105733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.098148 restraints weight = 4835.810| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.85 r_work: 0.3082 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 3238 Z= 0.094 Angle : 0.564 8.463 4422 Z= 0.264 Chirality : 0.042 0.148 483 Planarity : 0.003 0.032 568 Dihedral : 3.744 19.585 455 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.03 % Allowed : 14.19 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.41), residues: 409 helix: -3.63 (0.70), residues: 26 sheet: 0.95 (0.43), residues: 138 loop : 0.21 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 19 TYR 0.008 0.001 TYR H 60 PHE 0.015 0.001 PHE E 490 TRP 0.010 0.001 TRP H 47 HIS 0.002 0.001 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00211 / 0.09 ( 3229) covalent geometry : angle 0.53972 / 0.26 ( 4401) SS BOND : bond 0.00171 / 0.09 ( 6) SS BOND : angle 1.02579 / 0.54 ( 12) hydrogen bonds : bond 0.02803 / 2.02 ( 98) hydrogen bonds : angle 5.46834 / 3.77 ( 234) link_BETA1-4 : bond 0.00107 / 0.06 ( 1) link_BETA1-4 : angle 5.09213 / 2.67 ( 3) link_BETA1-6 : bond 0.00782 / 0.41 ( 1) link_BETA1-6 : angle 1.33135 / 0.70 ( 3) link_NAG-ASN : bond 0.00251 / 0.13 ( 1) link_NAG-ASN : angle 3.00897 / 1.71 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1187.82 seconds wall clock time: 21 minutes 7.42 seconds (1267.42 seconds total)