Starting phenix.real_space_refine on Thu Oct 22 17:40:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9t74_55625/10_2026/9t74_55625.cif Found real_map, /net/cci-nas-00/data/ceres_data/9t74_55625/10_2026/9t74_55625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9t74_55625/10_2026/9t74_55625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9t74_55625/10_2026/9t74_55625.map" model { file = "/net/cci-nas-00/data/ceres_data/9t74_55625/10_2026/9t74_55625.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9t74_55625/10_2026/9t74_55625.cif" } resolution = 3.46 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= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians P 51 5.49 5 Mg 1 5.21 5 S 8 5.16 5 C 1501 2.51 5 N 452 2.21 5 O 634 1.98 5 F 26 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2673 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1084 Unusual residues: {'CFZ': 13} Classifications: {'DNA': 13, 'DNA_mixed': 13, 'RNA': 25} Modifications used: {'rna2p_pur': 2, 'rna3p_pur': 23} Link IDs: {'rna2p': 2, 'rna3p': 27, None: 21} Not linked: pdbres=" G A 85 " pdbres="CFZ A 86 " Not linked: pdbres="CFZ A 86 " pdbres=" G A 87 " Not linked: pdbres=" A A 88 " pdbres="CFZ A 89 " Not linked: pdbres="CFZ A 89 " pdbres=" A A 90 " Not linked: pdbres="UFT A 99 " pdbres="CFZ A 100 " ... (remaining 16 not shown) Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 78 Unresolved non-hydrogen dihedrals: 26 Chain: "B" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1560 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.99, per 1000 atoms: 0.37 Number of scatterers: 2673 At special positions: 0 Unit cell: (69.876, 59.2005, 103.843, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 8 16.00 P 51 15.00 Mg 1 11.99 F 26 9.00 O 634 8.00 N 452 7.00 C 1501 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " 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=21, symmetry=0 Links applied BETA1-4 " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG C 1 " - " ASN B 343 " Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.28 Conformation dependent library (CDL) restraints added in 66.4 milliseconds 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 364 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 3 sheets defined 15.7% alpha, 18.3% beta 1 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 Processing sheet with id=AA2, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 473 through 474 42 hydrogen bonds defined for protein. 105 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 0.38 Time building geometry restraints manager: 0.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 330 1.32 - 1.45: 1090 1.45 - 1.58: 1313 1.58 - 1.72: 80 1.72 - 1.85: 8 Bond restraints: 2821 Sorted by residual: bond pdb=" N1 UFT A 98 " pdb=" C6 UFT A 98 " ideal model delta sigma weight residual 1.364 1.487 -0.123 2.00e-02 2.50e+03 3.77e+01 bond pdb=" N1 UFT A 91 " pdb=" C6 UFT A 91 " ideal model delta sigma weight residual 1.364 1.487 -0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" N1 UFT A 92 " pdb=" C6 UFT A 92 " ideal model delta sigma weight residual 1.364 1.486 -0.122 2.00e-02 2.50e+03 3.75e+01 bond pdb=" N1 UFT A 110 " pdb=" C6 UFT A 110 " ideal model delta sigma weight residual 1.364 1.486 -0.122 2.00e-02 2.50e+03 3.72e+01 bond pdb=" N1 UFT A 113 " pdb=" C6 UFT A 113 " ideal model delta sigma weight residual 1.364 1.486 -0.122 2.00e-02 2.50e+03 3.71e+01 ... (remaining 2816 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 3634 2.83 - 5.66: 217 5.66 - 8.50: 92 8.50 - 11.33: 29 11.33 - 14.16: 48 Bond angle restraints: 4020 Sorted by residual: angle pdb=" O2P CFZ A 107 " pdb=" P CFZ A 107 " pdb=" O5' CFZ A 107 " ideal model delta sigma weight residual 99.98 114.14 -14.16 3.00e+00 1.11e-01 2.23e+01 angle pdb=" O2P CFZ A 86 " pdb=" P CFZ A 86 " pdb=" O5' CFZ A 86 " ideal model delta sigma weight residual 99.98 114.11 -14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" OP1 UFT A 91 " pdb=" P UFT A 91 " pdb=" OP2 UFT A 91 " ideal model delta sigma weight residual 116.95 102.85 14.10 3.00e+00 1.11e-01 2.21e+01 angle pdb=" O2P CFZ A 133 " pdb=" P CFZ A 133 " pdb=" O5' CFZ A 133 " ideal model delta sigma weight residual 99.98 113.99 -14.01 3.00e+00 1.11e-01 2.18e+01 angle pdb=" O2P CFZ A 89 " pdb=" P CFZ A 89 " pdb=" O5' CFZ A 89 " ideal model delta sigma weight residual 99.98 113.98 -14.00 3.00e+00 1.11e-01 2.18e+01 ... (remaining 4015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 1837 35.16 - 70.32: 164 70.32 - 105.48: 17 105.48 - 140.64: 5 140.64 - 175.79: 10 Dihedral angle restraints: 2033 sinusoidal: 1458 harmonic: 575 Sorted by residual: dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 24.12 68.88 1 1.00e+01 1.00e-02 6.14e+01 dihedral pdb=" CA CYS B 336 " pdb=" C CYS B 336 " pdb=" N PRO B 337 " pdb=" CA PRO B 337 " ideal model delta harmonic sigma weight residual -180.00 -155.01 -24.99 0 5.00e+00 4.00e-02 2.50e+01 dihedral pdb=" O5' CFZ A 100 " pdb=" C5' CFZ A 100 " pdb=" C4' CFZ A 100 " pdb=" C3' CFZ A 100 " ideal model delta sinusoidal sigma weight residual 51.22 -124.57 175.79 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 338 0.063 - 0.125: 64 0.125 - 0.188: 33 0.188 - 0.250: 17 0.250 - 0.313: 17 Chirality restraints: 469 Sorted by residual: chirality pdb=" C2' UFT A 118 " pdb=" C3' UFT A 118 " pdb=" C1' UFT A 118 " pdb=" F2' UFT A 118 " both_signs ideal model delta sigma weight residual False 2.71 2.39 0.31 2.00e-01 2.50e+01 2.44e+00 chirality pdb=" C2' UFT A 113 " pdb=" C3' UFT A 113 " pdb=" C1' UFT A 113 " pdb=" F2' UFT A 113 " both_signs ideal model delta sigma weight residual False 2.71 2.40 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" C3' UFT A 113 " pdb=" C4' UFT A 113 " pdb=" O3' UFT A 113 " pdb=" C2' UFT A 113 " both_signs ideal model delta sigma weight residual False -2.29 -2.59 0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 466 not shown) Planarity restraints: 340 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 468 " -0.009 2.00e-02 2.50e+03 1.79e-02 3.19e+00 pdb=" C ILE B 468 " 0.031 2.00e-02 2.50e+03 pdb=" O ILE B 468 " -0.011 2.00e-02 2.50e+03 pdb=" N SER B 469 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 470 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.85e+00 pdb=" C THR B 470 " 0.029 2.00e-02 2.50e+03 pdb=" O THR B 470 " -0.011 2.00e-02 2.50e+03 pdb=" N GLU B 471 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 500 " -0.008 2.00e-02 2.50e+03 1.52e-02 2.30e+00 pdb=" C THR B 500 " 0.026 2.00e-02 2.50e+03 pdb=" O THR B 500 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN B 501 " -0.009 2.00e-02 2.50e+03 ... (remaining 337 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 297 2.75 - 3.29: 2574 3.29 - 3.82: 4953 3.82 - 4.36: 5788 4.36 - 4.90: 8691 Nonbonded interactions: 22303 Sorted by model distance: nonbonded pdb=" OP2 UFT A 95 " pdb="MG MG A 201 " model vdw 2.209 2.170 nonbonded pdb=" OP2 A A 96 " pdb="MG MG A 201 " model vdw 2.222 2.170 nonbonded pdb=" OP2 G A 128 " pdb=" N2 G A 128 " model vdw 2.229 3.120 nonbonded pdb=" O ASP B 442 " pdb=" ND2 ASN B 448 " model vdw 2.252 3.120 nonbonded pdb=" OD1 ASN B 448 " pdb=" ND2 ASN B 450 " model vdw 2.316 3.120 ... (remaining 22298 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: 21.330 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.820 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 0.026 0.123 2848 Z= 1.346 Angle : 2.261 14.159 4034 Z= 0.875 Chirality : 0.089 0.313 469 Planarity : 0.004 0.028 339 Dihedral : 26.596 175.794 1657 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.29 % Allowed : 20.00 % Favored : 74.71 % 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: -1.02 (0.63), residues: 195 helix: -3.03 (0.70), residues: 39 sheet: -0.30 (0.94), residues: 36 loop : 0.18 (0.60), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 408 TYR 0.006 0.001 TYR B 453 PHE 0.006 0.001 PHE B 377 TRP 0.006 0.001 TRP B 436 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.02550 / 1.28 ( 2821) covalent geometry : angle 2.26269 / 0.88 ( 4020) SS BOND : bond 0.00739 / 0.37 ( 4) SS BOND : angle 1.99609 / 3.80 ( 8) hydrogen bonds : bond 0.13811 / 14.86 ( 44) hydrogen bonds : angle 9.71409 / 11.57 ( 105) Misc. bond : bond 0.05056 / 5.35 ( 21) link_BETA1-4 : bond 0.00481 / 0.24 ( 1) link_BETA1-4 : angle 1.30009 / 2.31 ( 3) link_NAG-ASN : bond 0.00148 / 0.07 ( 1) link_NAG-ASN : angle 0.99343 / 1.77 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.076 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 36 average time/residue: 0.0754 time to fit residues: 3.1715 Evaluate side-chains 26 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 433 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: [12, 13, 1, 8, 16, 15, 9, 11, 18, 6, 4] chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.2980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 15 optimal weight: 0.0980 chunk 9 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 450 ASN ** B 506 GLN ** 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 = 0.3573 r_free = 0.3573 target = 0.087347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.068464 restraints weight = 7582.384| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.40 r_work: 0.3001 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 2848 Z= 0.195 Angle : 0.870 7.376 4034 Z= 0.378 Chirality : 0.047 0.267 469 Planarity : 0.004 0.023 339 Dihedral : 26.875 176.365 1312 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 6.47 % Allowed : 22.35 % Favored : 71.18 % 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: -0.96 (0.62), residues: 195 helix: -2.80 (0.80), residues: 33 sheet: -0.51 (0.93), residues: 37 loop : 0.07 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.005 0.001 TYR B 453 PHE 0.007 0.001 PHE B 392 TRP 0.005 0.001 TRP B 436 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 2821) covalent geometry : angle 0.85983 / 0.37 ( 4020) SS BOND : bond 0.00884 / 0.48 ( 4) SS BOND : angle 2.97149 / 5.54 ( 8) hydrogen bonds : bond 0.03827 / 3.90 ( 44) hydrogen bonds : angle 7.95252 / 9.68 ( 105) Misc. bond : bond 0.00152 / 0.14 ( 21) link_BETA1-4 : bond 0.00284 / 0.14 ( 1) link_BETA1-4 : angle 1.26869 / 2.28 ( 3) link_NAG-ASN : bond 0.00069 / 0.03 ( 1) link_NAG-ASN : angle 1.10933 / 2.16 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 27 time to evaluate : 0.044 Fit side-chains revert: symmetry clash REVERT: B 458 LYS cc_start: 0.8842 (mmmm) cc_final: 0.8526 (tppt) outliers start: 11 outliers final: 7 residues processed: 36 average time/residue: 0.0824 time to fit residues: 3.4532 Evaluate side-chains 31 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: [0, 2, 21, 10, 9, 22, 1, 19, 3, 5, 8] chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 0.0980 chunk 10 optimal weight: 0.5980 chunk 9 optimal weight: 0.4980 chunk 22 optimal weight: 0.1980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 0.0770 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 8 optimal weight: 0.3980 overall best weight: 0.2338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 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 = 0.3580 r_free = 0.3580 target = 0.087507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.068275 restraints weight = 7588.769| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.37 r_work: 0.2998 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.1727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2848 Z= 0.138 Angle : 0.813 7.468 4034 Z= 0.361 Chirality : 0.044 0.253 469 Planarity : 0.004 0.025 339 Dihedral : 25.658 173.855 1311 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 4.71 % Allowed : 22.35 % Favored : 72.94 % 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: -0.79 (0.61), residues: 195 helix: -2.76 (0.92), residues: 27 sheet: -0.55 (0.92), residues: 39 loop : 0.11 (0.55), residues: 129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 346 TYR 0.012 0.001 TYR B 451 PHE 0.004 0.001 PHE B 347 TRP 0.008 0.001 TRP B 436 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.14 ( 2821) covalent geometry : angle 0.80631 / 0.36 ( 4020) SS BOND : bond 0.00867 / 0.47 ( 4) SS BOND : angle 2.32714 / 4.42 ( 8) hydrogen bonds : bond 0.03484 / 3.47 ( 44) hydrogen bonds : angle 7.72259 / 9.47 ( 105) Misc. bond : bond 0.00091 / 0.10 ( 21) link_BETA1-4 : bond 0.00316 / 0.16 ( 1) link_BETA1-4 : angle 1.23178 / 2.15 ( 3) link_NAG-ASN : bond 0.00049 / 0.02 ( 1) link_NAG-ASN : angle 0.94194 / 1.78 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.076 Fit side-chains REVERT: B 458 LYS cc_start: 0.8801 (mmmm) cc_final: 0.8501 (tppt) REVERT: B 498 GLN cc_start: 0.8583 (mm-40) cc_final: 0.8257 (mm110) outliers start: 8 outliers final: 5 residues processed: 32 average time/residue: 0.0930 time to fit residues: 3.4239 Evaluate side-chains 28 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: [9, 15, 4, 1, 13, 22, 2, 14, 18, 5, 3] chunk 9 optimal weight: 0.0870 chunk 15 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 22 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 5 optimal weight: 0.4980 chunk 3 optimal weight: 1.9990 overall best weight: 0.3558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 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 = 0.3543 r_free = 0.3543 target = 0.085470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.066365 restraints weight = 7512.899| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.35 r_work: 0.2958 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2848 Z= 0.171 Angle : 0.787 7.947 4034 Z= 0.351 Chirality : 0.043 0.251 469 Planarity : 0.003 0.018 339 Dihedral : 24.981 178.169 1309 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 5.88 % Allowed : 21.18 % Favored : 72.94 % 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: -0.60 (0.63), residues: 195 helix: -2.90 (0.79), residues: 33 sheet: 0.05 (0.90), residues: 40 loop : 0.33 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 457 TYR 0.014 0.001 TYR B 451 PHE 0.005 0.001 PHE B 400 TRP 0.004 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.17 ( 2821) covalent geometry : angle 0.77844 / 0.35 ( 4020) SS BOND : bond 0.00748 / 0.39 ( 4) SS BOND : angle 2.60791 / 4.92 ( 8) hydrogen bonds : bond 0.03667 / 3.69 ( 44) hydrogen bonds : angle 7.51807 / 9.34 ( 105) Misc. bond : bond 0.00106 / 0.11 ( 21) link_BETA1-4 : bond 0.00276 / 0.14 ( 1) link_BETA1-4 : angle 1.27665 / 2.34 ( 3) link_NAG-ASN : bond 0.00172 / 0.09 ( 1) link_NAG-ASN : angle 1.09023 / 2.06 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.079 Fit side-chains REVERT: B 458 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8555 (tppt) outliers start: 10 outliers final: 7 residues processed: 33 average time/residue: 0.0824 time to fit residues: 3.1325 Evaluate side-chains 31 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: [6, 8, 11, 20, 16, 14, 22, 19, 13, 17, 10] chunk 6 optimal weight: 0.0770 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 19 optimal weight: 0.0050 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 overall best weight: 0.2352 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 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 = 0.3557 r_free = 0.3557 target = 0.086235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.067133 restraints weight = 7476.083| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.36 r_work: 0.2978 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2848 Z= 0.130 Angle : 0.758 7.900 4034 Z= 0.338 Chirality : 0.042 0.247 469 Planarity : 0.003 0.021 339 Dihedral : 24.364 178.702 1309 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.71 % Allowed : 24.12 % Favored : 71.18 % 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: -0.72 (0.61), residues: 195 helix: -3.08 (0.68), residues: 39 sheet: 0.01 (0.95), residues: 36 loop : 0.46 (0.57), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 346 TYR 0.012 0.001 TYR B 451 PHE 0.005 0.001 PHE B 377 TRP 0.007 0.001 TRP B 436 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 2821) covalent geometry : angle 0.75140 / 0.33 ( 4020) SS BOND : bond 0.00838 / 0.44 ( 4) SS BOND : angle 2.24879 / 4.25 ( 8) hydrogen bonds : bond 0.03182 / 3.21 ( 44) hydrogen bonds : angle 7.51183 / 9.30 ( 105) Misc. bond : bond 0.00075 / 0.08 ( 21) link_BETA1-4 : bond 0.00314 / 0.16 ( 1) link_BETA1-4 : angle 1.16820 / 2.07 ( 3) link_NAG-ASN : bond 0.00071 / 0.04 ( 1) link_NAG-ASN : angle 0.88867 / 1.67 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.078 Fit side-chains REVERT: B 458 LYS cc_start: 0.8862 (mmmm) cc_final: 0.8561 (tppt) outliers start: 8 outliers final: 6 residues processed: 32 average time/residue: 0.0861 time to fit residues: 3.1777 Evaluate side-chains 29 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: [7, 15, 20, 5, 11, 1, 14, 10, 17, 12, 16] chunk 7 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 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 = 0.3538 r_free = 0.3538 target = 0.085278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.065987 restraints weight = 7533.710| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.38 r_work: 0.2946 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2848 Z= 0.174 Angle : 0.763 8.333 4034 Z= 0.343 Chirality : 0.042 0.249 469 Planarity : 0.004 0.019 339 Dihedral : 23.779 179.303 1308 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.71 % Allowed : 24.12 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.63), residues: 195 helix: -2.81 (0.82), residues: 33 sheet: 0.02 (0.91), residues: 40 loop : 0.58 (0.58), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.013 0.001 TYR B 451 PHE 0.003 0.001 PHE B 377 TRP 0.005 0.001 TRP B 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 2821) covalent geometry : angle 0.75518 / 0.34 ( 4020) SS BOND : bond 0.00999 / 0.51 ( 4) SS BOND : angle 2.48294 / 4.64 ( 8) hydrogen bonds : bond 0.03548 / 3.57 ( 44) hydrogen bonds : angle 7.46744 / 9.32 ( 105) Misc. bond : bond 0.00075 / 0.09 ( 21) link_BETA1-4 : bond 0.00269 / 0.13 ( 1) link_BETA1-4 : angle 1.25416 / 2.30 ( 3) link_NAG-ASN : bond 0.00092 / 0.05 ( 1) link_NAG-ASN : angle 1.02070 / 1.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.096 Fit side-chains REVERT: B 458 LYS cc_start: 0.8907 (mmmm) cc_final: 0.8641 (tppt) outliers start: 8 outliers final: 7 residues processed: 31 average time/residue: 0.0912 time to fit residues: 3.2399 Evaluate side-chains 30 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: [8, 19, 11, 14, 17, 6, 21, 13, 1, 10, 3] chunk 8 optimal weight: 0.3980 chunk 19 optimal weight: 0.3980 chunk 11 optimal weight: 0.0870 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 6 optimal weight: 0.0570 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 overall best weight: 0.2476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 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 = 0.3553 r_free = 0.3553 target = 0.086017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.066877 restraints weight = 7472.976| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 2.37 r_work: 0.2971 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2848 Z= 0.132 Angle : 0.743 8.078 4034 Z= 0.335 Chirality : 0.042 0.245 469 Planarity : 0.003 0.022 339 Dihedral : 23.274 177.874 1308 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 5.88 % Allowed : 24.71 % Favored : 69.41 % 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: -0.51 (0.62), residues: 195 helix: -3.14 (0.71), residues: 39 sheet: -0.01 (0.94), residues: 36 loop : 0.75 (0.58), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.011 0.001 TYR B 451 PHE 0.004 0.001 PHE B 347 TRP 0.008 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 2821) covalent geometry : angle 0.73664 / 0.33 ( 4020) SS BOND : bond 0.00696 / 0.37 ( 4) SS BOND : angle 2.19314 / 4.12 ( 8) hydrogen bonds : bond 0.03128 / 3.22 ( 44) hydrogen bonds : angle 7.48092 / 9.30 ( 105) Misc. bond : bond 0.00048 / 0.05 ( 21) link_BETA1-4 : bond 0.00267 / 0.13 ( 1) link_BETA1-4 : angle 1.19824 / 2.13 ( 3) link_NAG-ASN : bond 0.00032 / 0.02 ( 1) link_NAG-ASN : angle 0.91549 / 1.72 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.077 Fit side-chains REVERT: B 458 LYS cc_start: 0.8901 (mmmm) cc_final: 0.8651 (tppt) outliers start: 10 outliers final: 9 residues processed: 33 average time/residue: 0.0831 time to fit residues: 3.1816 Evaluate side-chains 33 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: [15, 2, 20, 7, 18, 14, 1, 6, 8, 22, 3] chunk 15 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 7 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 22 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 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 = 0.3534 r_free = 0.3534 target = 0.085051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.065830 restraints weight = 7700.270| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.39 r_work: 0.2947 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 2848 Z= 0.183 Angle : 0.769 8.120 4034 Z= 0.350 Chirality : 0.042 0.249 469 Planarity : 0.004 0.021 339 Dihedral : 22.960 177.257 1308 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 6.47 % Allowed : 23.53 % Favored : 70.00 % 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: -0.33 (0.64), residues: 195 helix: -2.85 (0.85), residues: 33 sheet: 0.10 (0.92), residues: 40 loop : 0.63 (0.59), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.013 0.001 TYR B 451 PHE 0.004 0.001 PHE B 377 TRP 0.006 0.001 TRP B 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.18 ( 2821) covalent geometry : angle 0.76117 / 0.35 ( 4020) SS BOND : bond 0.00893 / 0.46 ( 4) SS BOND : angle 2.52822 / 4.73 ( 8) hydrogen bonds : bond 0.03491 / 3.48 ( 44) hydrogen bonds : angle 7.43814 / 9.32 ( 105) Misc. bond : bond 0.00065 / 0.07 ( 21) link_BETA1-4 : bond 0.00240 / 0.12 ( 1) link_BETA1-4 : angle 1.25386 / 2.30 ( 3) link_NAG-ASN : bond 0.00056 / 0.03 ( 1) link_NAG-ASN : angle 1.00586 / 1.88 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.079 Fit side-chains REVERT: B 458 LYS cc_start: 0.8916 (mmmm) cc_final: 0.8672 (tppt) outliers start: 11 outliers final: 8 residues processed: 34 average time/residue: 0.0886 time to fit residues: 3.4794 Evaluate side-chains 32 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 24 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 390 LEU Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: [19, 4, 12, 21, 13, 1, 8, 9, 6, 11, 10] chunk 19 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 12 optimal weight: 0.0270 chunk 21 optimal weight: 0.1980 chunk 13 optimal weight: 0.0870 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 0.0980 chunk 9 optimal weight: 0.0980 chunk 6 optimal weight: 0.0470 chunk 11 optimal weight: 0.0980 chunk 10 optimal weight: 0.9990 overall best weight: 0.0714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 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 = 0.3575 r_free = 0.3575 target = 0.087166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.068060 restraints weight = 7667.612| |-----------------------------------------------------------------------------| r_work (start): 0.3144 rms_B_bonded: 2.40 r_work: 0.2999 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2848 Z= 0.119 Angle : 0.755 8.984 4034 Z= 0.343 Chirality : 0.041 0.242 469 Planarity : 0.004 0.025 339 Dihedral : 22.281 173.558 1308 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 6.47 % Allowed : 24.12 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.45 (0.63), residues: 195 helix: -3.16 (0.71), residues: 39 sheet: 0.03 (0.94), residues: 36 loop : 0.82 (0.59), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 346 TYR 0.011 0.001 TYR B 451 PHE 0.005 0.001 PHE B 347 TRP 0.009 0.002 TRP B 436 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.12 ( 2821) covalent geometry : angle 0.75034 / 0.34 ( 4020) SS BOND : bond 0.00808 / 0.42 ( 4) SS BOND : angle 1.99287 / 3.78 ( 8) hydrogen bonds : bond 0.02857 / 3.06 ( 44) hydrogen bonds : angle 7.52316 / 9.33 ( 105) Misc. bond : bond 0.00040 / 0.04 ( 21) link_BETA1-4 : bond 0.00294 / 0.15 ( 1) link_BETA1-4 : angle 1.11201 / 1.97 ( 3) link_NAG-ASN : bond 0.00204 / 0.10 ( 1) link_NAG-ASN : angle 0.84552 / 1.55 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.051 Fit side-chains REVERT: B 458 LYS cc_start: 0.8857 (mmmm) cc_final: 0.8621 (tppt) outliers start: 11 outliers final: 10 residues processed: 33 average time/residue: 0.0715 time to fit residues: 2.7166 Evaluate side-chains 34 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 428 ASP Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: [6, 9, 2, 16, 3, 22, 5, 17, 13, 8, 11] chunk 6 optimal weight: 0.0000 chunk 9 optimal weight: 0.2980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.0980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 0.0770 chunk 8 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 overall best weight: 0.1140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 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 = 0.3584 r_free = 0.3584 target = 0.087656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.068692 restraints weight = 7713.233| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.41 r_work: 0.3012 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2848 Z= 0.119 Angle : 0.731 7.805 4034 Z= 0.338 Chirality : 0.041 0.245 469 Planarity : 0.003 0.023 339 Dihedral : 21.747 173.169 1308 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.12 % Allowed : 25.29 % Favored : 70.59 % 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: -0.47 (0.63), residues: 195 helix: -2.92 (0.82), residues: 33 sheet: -0.06 (0.94), residues: 37 loop : 0.52 (0.58), residues: 125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 346 TYR 0.011 0.001 TYR B 451 PHE 0.003 0.001 PHE B 456 TRP 0.007 0.001 TRP B 436 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 2821) covalent geometry : angle 0.72542 / 0.34 ( 4020) SS BOND : bond 0.00720 / 0.37 ( 4) SS BOND : angle 2.10254 / 3.97 ( 8) hydrogen bonds : bond 0.03085 / 3.14 ( 44) hydrogen bonds : angle 7.40113 / 9.20 ( 105) Misc. bond : bond 0.00040 / 0.04 ( 21) link_BETA1-4 : bond 0.00304 / 0.15 ( 1) link_BETA1-4 : angle 1.15374 / 2.09 ( 3) link_NAG-ASN : bond 0.00090 / 0.04 ( 1) link_NAG-ASN : angle 0.92643 / 1.65 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 390 Ramachandran restraints generated. 195 Oldfield, 0 Emsley, 195 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 24 time to evaluate : 0.075 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 31 average time/residue: 0.0967 time to fit residues: 3.4943 Evaluate side-chains 30 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 332 ILE Chi-restraints excluded: chain B residue 338 PHE Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 415 THR Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain B residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: [23, 15, 18, 22, 5, 11, 7, 4, 0, 16, 19] chunk 23 optimal weight: 0.9990 chunk 15 optimal weight: 0.0870 chunk 18 optimal weight: 0.0000 chunk 22 optimal weight: 0.2980 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 overall best weight: 0.2562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 506 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 = 0.3541 r_free = 0.3541 target = 0.086095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.066402 restraints weight = 7726.536| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.64 r_work: 0.2936 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 2848 Z= 0.139 Angle : 0.734 7.975 4034 Z= 0.336 Chirality : 0.041 0.247 469 Planarity : 0.003 0.024 339 Dihedral : 21.497 171.346 1308 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 4.12 % Allowed : 25.88 % Favored : 70.00 % 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: -0.43 (0.64), residues: 195 helix: -3.18 (0.69), residues: 39 sheet: 0.08 (0.94), residues: 36 loop : 0.83 (0.61), residues: 120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 346 TYR 0.010 0.001 TYR B 451 PHE 0.004 0.001 PHE B 456 TRP 0.007 0.001 TRP B 436 HIS 0.000 0.000 HIS B 519 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 2821) covalent geometry : angle 0.72716 / 0.33 ( 4020) SS BOND : bond 0.00823 / 0.43 ( 4) SS BOND : angle 2.22674 / 4.18 ( 8) hydrogen bonds : bond 0.03207 / 3.23 ( 44) hydrogen bonds : angle 7.43378 / 9.23 ( 105) Misc. bond : bond 0.00044 / 0.05 ( 21) link_BETA1-4 : bond 0.00267 / 0.13 ( 1) link_BETA1-4 : angle 1.14127 / 2.07 ( 3) link_NAG-ASN : bond 0.00031 / 0.02 ( 1) link_NAG-ASN : angle 0.92416 / 1.70 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1251.37 seconds wall clock time: 22 minutes 14.30 seconds (1334.30 seconds total)