Starting phenix.real_space_refine on Tue Mar 3 12:17:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dnw_27582/03_2026/8dnw_27582.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dnw_27582/03_2026/8dnw_27582.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dnw_27582/03_2026/8dnw_27582.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dnw_27582/03_2026/8dnw_27582.map" model { file = "/net/cci-nas-00/data/ceres_data/8dnw_27582/03_2026/8dnw_27582.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dnw_27582/03_2026/8dnw_27582.cif" } resolution = 3.4 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= 0.003 sd= 0.033 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 26 5.16 5 C 2689 2.51 5 N 647 2.21 5 O 698 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4060 Number of models: 1 Model: "" Number of chains: 3 Chain: "B" Number of atoms: 457 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 457 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 2, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 28 Chain: "C" Number of atoms: 251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 251 Classifications: {'peptide': 32} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 29} Chain: "A" Number of atoms: 3352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 435, 3352 Classifications: {'peptide': 435} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 416} Chain breaks: 4 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 25 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 1.09, per 1000 atoms: 0.27 Number of scatterers: 4060 At special positions: 0 Unit cell: (95.55, 79.8, 77.7, 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 26 16.00 O 698 8.00 N 647 7.00 C 2689 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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 Time building additional restraints: 0.33 Conformation dependent library (CDL) restraints added in 154.4 milliseconds 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 968 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 76.9% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'B' and resid 7 through 25 Processing helix chain 'B' and resid 29 through 66 Proline residue: B 60 - end of helix Processing helix chain 'C' and resid 69 through 96 removed outlier: 3.644A pdb=" N VAL C 73 " --> pdb=" O GLY C 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 27 through 46 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 70 Processing helix chain 'A' and resid 75 through 79 removed outlier: 4.556A pdb=" N LEU A 79 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 98 Processing helix chain 'A' and resid 110 through 135 removed outlier: 4.312A pdb=" N GLY A 135 " --> pdb=" O TYR A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 171 removed outlier: 5.999A pdb=" N ALA A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.966A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N ILE A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 197 removed outlier: 3.616A pdb=" N LEU A 181 " --> pdb=" O SER A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 228 through 235 Processing helix chain 'A' and resid 241 through 260 removed outlier: 3.578A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 288 through 312 Processing helix chain 'A' and resid 316 through 321 Processing helix chain 'A' and resid 340 through 346 Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.897A pdb=" N GLU A 381 " --> pdb=" O LYS A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 408 through 438 removed outlier: 3.557A pdb=" N GLU A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 443 through 467 Processing sheet with id=AA1, first strand: chain 'C' and resid 66 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA3, first strand: chain 'A' and resid 277 through 282 removed outlier: 3.932A pdb=" N GLY A 277 " --> pdb=" O ILE A 267 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ILE A 267 " --> pdb=" O GLY A 277 " (cutoff:3.500A) 310 hydrogen bonds defined for protein. 924 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: 0.61 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1231 1.34 - 1.46: 964 1.46 - 1.58: 1908 1.58 - 1.70: 0 1.70 - 1.81: 43 Bond restraints: 4146 Sorted by residual: bond pdb=" CA ILE A 281 " pdb=" CB ILE A 281 " ideal model delta sigma weight residual 1.540 1.526 0.014 1.36e-02 5.41e+03 1.12e+00 bond pdb=" CG GLU B 32 " pdb=" CD GLU B 32 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.42e-01 bond pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " ideal model delta sigma weight residual 1.520 1.546 -0.026 3.00e-02 1.11e+03 7.79e-01 bond pdb=" CG1 ILE A 48 " pdb=" CD1 ILE A 48 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.71e-01 bond pdb=" CA ILE A 441 " pdb=" CB ILE A 441 " ideal model delta sigma weight residual 1.537 1.528 0.009 1.25e-02 6.40e+03 5.65e-01 ... (remaining 4141 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 5514 1.51 - 3.02: 80 3.02 - 4.53: 17 4.53 - 6.04: 6 6.04 - 7.55: 1 Bond angle restraints: 5618 Sorted by residual: angle pdb=" CB MET A 91 " pdb=" CG MET A 91 " pdb=" SD MET A 91 " ideal model delta sigma weight residual 112.70 105.15 7.55 3.00e+00 1.11e-01 6.33e+00 angle pdb=" CB GLU B 32 " pdb=" CG GLU B 32 " pdb=" CD GLU B 32 " ideal model delta sigma weight residual 112.60 116.42 -3.82 1.70e+00 3.46e-01 5.04e+00 angle pdb=" N VAL A 382 " pdb=" CA VAL A 382 " pdb=" C VAL A 382 " ideal model delta sigma weight residual 111.00 113.37 -2.37 1.09e+00 8.42e-01 4.74e+00 angle pdb=" N GLY A 442 " pdb=" CA GLY A 442 " pdb=" C GLY A 442 " ideal model delta sigma weight residual 115.27 112.28 2.99 1.41e+00 5.03e-01 4.49e+00 angle pdb=" C ILE A 90 " pdb=" N MET A 91 " pdb=" CA MET A 91 " ideal model delta sigma weight residual 121.14 117.56 3.58 1.75e+00 3.27e-01 4.18e+00 ... (remaining 5613 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.19: 2133 13.19 - 26.37: 217 26.37 - 39.56: 73 39.56 - 52.75: 17 52.75 - 65.93: 3 Dihedral angle restraints: 2443 sinusoidal: 936 harmonic: 1507 Sorted by residual: dihedral pdb=" CA THR A 286 " pdb=" C THR A 286 " pdb=" N SER A 287 " pdb=" CA SER A 287 " ideal model delta harmonic sigma weight residual -180.00 -164.08 -15.92 0 5.00e+00 4.00e-02 1.01e+01 dihedral pdb=" CA ASN A 241 " pdb=" C ASN A 241 " pdb=" N LEU A 242 " pdb=" CA LEU A 242 " ideal model delta harmonic sigma weight residual 180.00 165.48 14.52 0 5.00e+00 4.00e-02 8.43e+00 dihedral pdb=" CB LYS A 392 " pdb=" CG LYS A 392 " pdb=" CD LYS A 392 " pdb=" CE LYS A 392 " ideal model delta sinusoidal sigma weight residual 60.00 105.11 -45.11 3 1.50e+01 4.44e-03 8.11e+00 ... (remaining 2440 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 423 0.031 - 0.062: 173 0.062 - 0.092: 56 0.092 - 0.123: 15 0.123 - 0.154: 2 Chirality restraints: 669 Sorted by residual: chirality pdb=" CA MET A 91 " pdb=" N MET A 91 " pdb=" C MET A 91 " pdb=" CB MET A 91 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.92e-01 chirality pdb=" CA ILE A 48 " pdb=" N ILE A 48 " pdb=" C ILE A 48 " pdb=" CB ILE A 48 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CA ILE A 281 " pdb=" N ILE A 281 " pdb=" C ILE A 281 " pdb=" CB ILE A 281 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 ... (remaining 666 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 9 " 0.034 5.00e-02 4.00e+02 5.21e-02 4.34e+00 pdb=" N PRO B 10 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 10 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 10 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 239 " -0.028 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO A 240 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 71 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO C 72 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO C 72 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 72 " 0.021 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 13 2.56 - 3.15: 3351 3.15 - 3.73: 6573 3.73 - 4.32: 8301 4.32 - 4.90: 14462 Nonbonded interactions: 32700 Sorted by model distance: nonbonded pdb=" OE1 GLU A 78 " pdb=" OH TYR A 137 " model vdw 1.976 3.040 nonbonded pdb=" OD2 ASP A 139 " pdb=" OG SER A 141 " model vdw 2.152 3.040 nonbonded pdb=" OG1 THR B 26 " pdb=" OE2 GLU A 264 " model vdw 2.252 3.040 nonbonded pdb=" O VAL A 130 " pdb=" OG1 THR A 134 " model vdw 2.256 3.040 nonbonded pdb=" N THR A 323 " pdb=" O GLY A 339 " model vdw 2.358 3.120 ... (remaining 32695 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: 1.380 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.260 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 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 : 0.003 0.029 4146 Z= 0.133 Angle : 0.515 7.549 5618 Z= 0.269 Chirality : 0.038 0.154 669 Planarity : 0.004 0.052 687 Dihedral : 12.461 65.934 1475 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 2.85 (0.37), residues: 514 helix: 2.59 (0.26), residues: 384 sheet: -2.76 (1.69), residues: 7 loop : -0.12 (0.61), residues: 123 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 95 TYR 0.006 0.001 TYR A 457 PHE 0.015 0.001 PHE C 85 TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4146) covalent geometry : angle 0.51461 ( 5618) hydrogen bonds : bond 0.10182 ( 310) hydrogen bonds : angle 4.85658 ( 924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.133 Fit side-chains REVERT: B 38 MET cc_start: 0.7454 (tmm) cc_final: 0.6989 (tmm) REVERT: C 76 MET cc_start: 0.7862 (ttp) cc_final: 0.7595 (ttm) REVERT: A 64 TRP cc_start: 0.8316 (m100) cc_final: 0.8109 (m100) outliers start: 0 outliers final: 0 residues processed: 62 average time/residue: 0.0525 time to fit residues: 4.2855 Evaluate side-chains 53 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.150685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.122868 restraints weight = 5350.981| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.89 r_work: 0.3174 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4146 Z= 0.130 Angle : 0.502 7.180 5618 Z= 0.255 Chirality : 0.038 0.149 669 Planarity : 0.004 0.046 687 Dihedral : 3.596 15.329 557 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 0.92 % Allowed : 6.68 % Favored : 92.40 % 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: 2.97 (0.37), residues: 514 helix: 2.62 (0.25), residues: 388 sheet: -2.72 (1.68), residues: 7 loop : 0.04 (0.62), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 30 TYR 0.007 0.001 TYR A 457 PHE 0.023 0.001 PHE A 156 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 4146) covalent geometry : angle 0.50174 ( 5618) hydrogen bonds : bond 0.03479 ( 310) hydrogen bonds : angle 4.02948 ( 924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.111 Fit side-chains REVERT: B 38 MET cc_start: 0.7745 (tmm) cc_final: 0.7149 (tmm) REVERT: C 76 MET cc_start: 0.8584 (ttp) cc_final: 0.8169 (ttm) REVERT: C 86 MET cc_start: 0.8066 (mmm) cc_final: 0.7801 (mmm) REVERT: A 139 ASP cc_start: 0.8197 (t0) cc_final: 0.7990 (t0) REVERT: A 149 LEU cc_start: 0.8600 (tt) cc_final: 0.8252 (tt) REVERT: A 324 TRP cc_start: 0.8281 (m100) cc_final: 0.8039 (m100) outliers start: 4 outliers final: 3 residues processed: 60 average time/residue: 0.0465 time to fit residues: 3.7034 Evaluate side-chains 58 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 55 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 406 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 4 optimal weight: 0.5980 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 41 optimal weight: 10.0000 chunk 26 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 48 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.151349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.123067 restraints weight = 5275.748| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.92 r_work: 0.3157 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4146 Z= 0.130 Angle : 0.493 6.828 5618 Z= 0.245 Chirality : 0.038 0.139 669 Planarity : 0.004 0.042 687 Dihedral : 3.540 15.444 557 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.15 % Allowed : 9.22 % Favored : 89.63 % 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: 3.02 (0.37), residues: 514 helix: 2.66 (0.25), residues: 388 sheet: -2.86 (1.57), residues: 7 loop : 0.04 (0.61), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.006 0.001 TYR A 457 PHE 0.020 0.001 PHE A 156 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4146) covalent geometry : angle 0.49295 ( 5618) hydrogen bonds : bond 0.03297 ( 310) hydrogen bonds : angle 3.88622 ( 924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.166 Fit side-chains REVERT: B 38 MET cc_start: 0.7814 (tmm) cc_final: 0.7172 (tmm) REVERT: C 76 MET cc_start: 0.8610 (ttp) cc_final: 0.8203 (ttm) REVERT: C 86 MET cc_start: 0.8133 (mmm) cc_final: 0.7819 (mmm) REVERT: A 139 ASP cc_start: 0.8332 (t0) cc_final: 0.8033 (t0) REVERT: A 149 LEU cc_start: 0.8649 (tt) cc_final: 0.8409 (tt) REVERT: A 153 ILE cc_start: 0.8787 (mm) cc_final: 0.8551 (mm) REVERT: A 324 TRP cc_start: 0.8374 (m100) cc_final: 0.8086 (m100) outliers start: 5 outliers final: 3 residues processed: 60 average time/residue: 0.0574 time to fit residues: 4.6406 Evaluate side-chains 60 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 2 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 38 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.150645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122518 restraints weight = 5260.409| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 1.90 r_work: 0.3173 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4146 Z= 0.128 Angle : 0.480 6.876 5618 Z= 0.240 Chirality : 0.038 0.138 669 Planarity : 0.004 0.041 687 Dihedral : 3.511 15.527 557 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.38 % Allowed : 10.60 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.01 (0.37), residues: 514 helix: 2.64 (0.25), residues: 388 sheet: -2.89 (1.45), residues: 7 loop : 0.13 (0.62), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.008 0.001 TYR A 457 PHE 0.016 0.001 PHE A 156 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4146) covalent geometry : angle 0.48000 ( 5618) hydrogen bonds : bond 0.03262 ( 310) hydrogen bonds : angle 3.84282 ( 924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.102 Fit side-chains REVERT: B 38 MET cc_start: 0.7843 (tmm) cc_final: 0.7197 (tmm) REVERT: C 76 MET cc_start: 0.8585 (ttp) cc_final: 0.8193 (ttm) REVERT: C 86 MET cc_start: 0.8133 (mmm) cc_final: 0.7781 (mmm) REVERT: A 139 ASP cc_start: 0.8347 (t0) cc_final: 0.8128 (t0) REVERT: A 149 LEU cc_start: 0.8644 (tt) cc_final: 0.8389 (tt) REVERT: A 153 ILE cc_start: 0.8784 (mm) cc_final: 0.8551 (mm) REVERT: A 324 TRP cc_start: 0.8388 (m100) cc_final: 0.8081 (m100) outliers start: 6 outliers final: 4 residues processed: 60 average time/residue: 0.0474 time to fit residues: 3.9657 Evaluate side-chains 63 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 46 optimal weight: 6.9990 chunk 2 optimal weight: 0.0020 chunk 27 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.148914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120522 restraints weight = 5317.414| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.89 r_work: 0.3226 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4146 Z= 0.120 Angle : 0.486 7.741 5618 Z= 0.239 Chirality : 0.037 0.135 669 Planarity : 0.004 0.040 687 Dihedral : 3.473 15.368 557 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.38 % Allowed : 12.21 % Favored : 86.41 % 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: 3.13 (0.37), residues: 514 helix: 2.72 (0.25), residues: 388 sheet: -2.94 (1.29), residues: 7 loop : 0.19 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.006 0.001 TYR A 457 PHE 0.015 0.001 PHE A 156 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4146) covalent geometry : angle 0.48645 ( 5618) hydrogen bonds : bond 0.03159 ( 310) hydrogen bonds : angle 3.78347 ( 924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.107 Fit side-chains REVERT: B 38 MET cc_start: 0.7878 (tmm) cc_final: 0.7236 (tmm) REVERT: C 76 MET cc_start: 0.8545 (ttp) cc_final: 0.8190 (ttm) REVERT: C 86 MET cc_start: 0.8167 (mmm) cc_final: 0.7946 (mmm) REVERT: A 139 ASP cc_start: 0.8350 (t0) cc_final: 0.8109 (t0) REVERT: A 149 LEU cc_start: 0.8635 (tt) cc_final: 0.8350 (tt) REVERT: A 153 ILE cc_start: 0.8796 (mm) cc_final: 0.8529 (mm) REVERT: A 186 ASN cc_start: 0.8010 (t0) cc_final: 0.7644 (t0) REVERT: A 324 TRP cc_start: 0.8369 (m100) cc_final: 0.8017 (m100) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.0539 time to fit residues: 4.6548 Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 10 optimal weight: 0.4980 chunk 33 optimal weight: 0.0370 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.149464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.121276 restraints weight = 5352.859| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.89 r_work: 0.3237 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4146 Z= 0.111 Angle : 0.479 8.559 5618 Z= 0.234 Chirality : 0.037 0.146 669 Planarity : 0.004 0.040 687 Dihedral : 3.452 15.224 557 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.84 % Allowed : 13.13 % Favored : 85.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.23 (0.37), residues: 514 helix: 2.79 (0.25), residues: 388 sheet: -2.68 (1.41), residues: 7 loop : 0.21 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.007 0.001 TYR A 457 PHE 0.014 0.001 PHE A 156 TRP 0.005 0.001 TRP A 64 HIS 0.001 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4146) covalent geometry : angle 0.47925 ( 5618) hydrogen bonds : bond 0.03090 ( 310) hydrogen bonds : angle 3.73072 ( 924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.131 Fit side-chains REVERT: B 38 MET cc_start: 0.7878 (tmm) cc_final: 0.7231 (tmm) REVERT: C 76 MET cc_start: 0.8553 (ttp) cc_final: 0.8223 (ttm) REVERT: C 86 MET cc_start: 0.8211 (mmm) cc_final: 0.7984 (mmm) REVERT: A 139 ASP cc_start: 0.8377 (t0) cc_final: 0.8135 (t0) REVERT: A 149 LEU cc_start: 0.8623 (tt) cc_final: 0.8334 (tt) REVERT: A 153 ILE cc_start: 0.8854 (mm) cc_final: 0.8580 (mm) REVERT: A 186 ASN cc_start: 0.8001 (t0) cc_final: 0.7668 (t0) REVERT: A 324 TRP cc_start: 0.8384 (m100) cc_final: 0.8034 (m100) outliers start: 8 outliers final: 5 residues processed: 64 average time/residue: 0.0487 time to fit residues: 4.2777 Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 35 optimal weight: 0.9990 chunk 13 optimal weight: 0.4980 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 0.0870 chunk 19 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.151281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.122692 restraints weight = 5398.381| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 1.94 r_work: 0.3175 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4146 Z= 0.111 Angle : 0.496 9.654 5618 Z= 0.239 Chirality : 0.037 0.158 669 Planarity : 0.004 0.039 687 Dihedral : 3.439 15.192 557 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.38 % Allowed : 14.29 % Favored : 84.33 % 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: 3.28 (0.37), residues: 514 helix: 2.81 (0.25), residues: 388 sheet: -2.61 (1.39), residues: 7 loop : 0.29 (0.63), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 30 TYR 0.006 0.001 TYR A 457 PHE 0.014 0.001 PHE A 156 TRP 0.008 0.001 TRP A 64 HIS 0.001 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4146) covalent geometry : angle 0.49633 ( 5618) hydrogen bonds : bond 0.03066 ( 310) hydrogen bonds : angle 3.69350 ( 924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.164 Fit side-chains REVERT: B 38 MET cc_start: 0.7874 (tmm) cc_final: 0.7214 (tmm) REVERT: C 76 MET cc_start: 0.8566 (ttp) cc_final: 0.8224 (ttm) REVERT: C 86 MET cc_start: 0.8258 (mmm) cc_final: 0.7988 (mmm) REVERT: A 139 ASP cc_start: 0.8410 (t0) cc_final: 0.8148 (t0) REVERT: A 149 LEU cc_start: 0.8631 (tt) cc_final: 0.8332 (tt) REVERT: A 153 ILE cc_start: 0.8822 (mm) cc_final: 0.8548 (mm) REVERT: A 186 ASN cc_start: 0.8063 (t0) cc_final: 0.7669 (t0) REVERT: A 324 TRP cc_start: 0.8448 (m100) cc_final: 0.8045 (m100) outliers start: 6 outliers final: 5 residues processed: 61 average time/residue: 0.0514 time to fit residues: 4.3594 Evaluate side-chains 62 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 57 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 48 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.150428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.121953 restraints weight = 5209.715| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.90 r_work: 0.3145 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4146 Z= 0.125 Angle : 0.514 10.330 5618 Z= 0.246 Chirality : 0.038 0.178 669 Planarity : 0.004 0.038 687 Dihedral : 3.466 15.692 557 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.38 % Allowed : 14.98 % Favored : 83.64 % 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: 3.27 (0.37), residues: 514 helix: 2.80 (0.25), residues: 388 sheet: -2.79 (1.43), residues: 7 loop : 0.34 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.007 0.001 TYR A 457 PHE 0.013 0.001 PHE A 156 TRP 0.006 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 4146) covalent geometry : angle 0.51448 ( 5618) hydrogen bonds : bond 0.03151 ( 310) hydrogen bonds : angle 3.69386 ( 924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.164 Fit side-chains REVERT: B 38 MET cc_start: 0.7835 (tmm) cc_final: 0.7168 (tmm) REVERT: C 76 MET cc_start: 0.8585 (ttp) cc_final: 0.8235 (ttm) REVERT: C 86 MET cc_start: 0.8279 (mmm) cc_final: 0.7993 (mmm) REVERT: A 139 ASP cc_start: 0.8375 (t0) cc_final: 0.8137 (t0) REVERT: A 149 LEU cc_start: 0.8642 (tt) cc_final: 0.8333 (tt) REVERT: A 153 ILE cc_start: 0.8753 (mm) cc_final: 0.8480 (mm) REVERT: A 186 ASN cc_start: 0.8064 (t0) cc_final: 0.7664 (t0) REVERT: A 324 TRP cc_start: 0.8458 (m100) cc_final: 0.8037 (m100) outliers start: 6 outliers final: 5 residues processed: 62 average time/residue: 0.0528 time to fit residues: 4.4764 Evaluate side-chains 63 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 58 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 38 optimal weight: 6.9990 chunk 23 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.148765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.119804 restraints weight = 5404.897| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.93 r_work: 0.3127 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4146 Z= 0.149 Angle : 0.544 10.841 5618 Z= 0.259 Chirality : 0.038 0.160 669 Planarity : 0.004 0.039 687 Dihedral : 3.539 16.703 557 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.07 % Allowed : 14.52 % Favored : 83.41 % 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: 3.15 (0.37), residues: 514 helix: 2.70 (0.25), residues: 388 sheet: -3.01 (1.41), residues: 7 loop : 0.37 (0.65), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.008 0.001 TYR A 457 PHE 0.014 0.001 PHE A 252 TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 4146) covalent geometry : angle 0.54356 ( 5618) hydrogen bonds : bond 0.03253 ( 310) hydrogen bonds : angle 3.73692 ( 924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.145 Fit side-chains REVERT: B 38 MET cc_start: 0.7877 (tmm) cc_final: 0.7218 (tmm) REVERT: C 76 MET cc_start: 0.8609 (ttp) cc_final: 0.8255 (ttm) REVERT: C 86 MET cc_start: 0.8274 (mmm) cc_final: 0.7962 (mmm) REVERT: A 139 ASP cc_start: 0.8448 (t0) cc_final: 0.8142 (t0) REVERT: A 149 LEU cc_start: 0.8677 (tt) cc_final: 0.8359 (tt) REVERT: A 153 ILE cc_start: 0.8807 (mm) cc_final: 0.8542 (mm) REVERT: A 186 ASN cc_start: 0.8056 (t0) cc_final: 0.7647 (t0) REVERT: A 324 TRP cc_start: 0.8490 (m100) cc_final: 0.8060 (m100) outliers start: 9 outliers final: 8 residues processed: 63 average time/residue: 0.0516 time to fit residues: 4.4790 Evaluate side-chains 67 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 59 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.0170 chunk 4 optimal weight: 0.6980 chunk 15 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 overall best weight: 0.4818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.151132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.122678 restraints weight = 5221.916| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.90 r_work: 0.3145 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4146 Z= 0.112 Angle : 0.517 11.780 5618 Z= 0.246 Chirality : 0.038 0.171 669 Planarity : 0.004 0.039 687 Dihedral : 3.520 15.663 557 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.38 % Allowed : 15.21 % Favored : 83.41 % 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: 3.25 (0.37), residues: 514 helix: 2.75 (0.25), residues: 388 sheet: -3.20 (1.42), residues: 7 loop : 0.45 (0.64), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.006 0.001 TYR A 457 PHE 0.013 0.001 PHE A 156 TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4146) covalent geometry : angle 0.51713 ( 5618) hydrogen bonds : bond 0.03108 ( 310) hydrogen bonds : angle 3.68992 ( 924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1028 Ramachandran restraints generated. 514 Oldfield, 0 Emsley, 514 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.159 Fit side-chains REVERT: B 38 MET cc_start: 0.7827 (tmm) cc_final: 0.7167 (tmm) REVERT: C 76 MET cc_start: 0.8576 (ttp) cc_final: 0.8216 (ttm) REVERT: C 86 MET cc_start: 0.8237 (mmm) cc_final: 0.7936 (mmm) REVERT: A 139 ASP cc_start: 0.8414 (t0) cc_final: 0.8116 (t0) REVERT: A 149 LEU cc_start: 0.8610 (tt) cc_final: 0.8284 (tt) REVERT: A 153 ILE cc_start: 0.8782 (mm) cc_final: 0.8490 (mm) REVERT: A 186 ASN cc_start: 0.8050 (t0) cc_final: 0.7660 (t0) REVERT: A 324 TRP cc_start: 0.8464 (m100) cc_final: 0.8038 (m100) outliers start: 6 outliers final: 6 residues processed: 59 average time/residue: 0.0544 time to fit residues: 4.3724 Evaluate side-chains 62 residues out of total 448 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 VAL Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 217 PHE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 400 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.147700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.119283 restraints weight = 5318.479| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.89 r_work: 0.3136 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4146 Z= 0.139 Angle : 0.526 11.450 5618 Z= 0.253 Chirality : 0.038 0.161 669 Planarity : 0.004 0.039 687 Dihedral : 3.566 16.107 557 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.38 % Allowed : 14.98 % Favored : 83.64 % 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: 3.16 (0.37), residues: 514 helix: 2.68 (0.25), residues: 388 sheet: -3.20 (1.47), residues: 7 loop : 0.46 (0.65), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 30 TYR 0.005 0.001 TYR A 457 PHE 0.012 0.001 PHE A 156 TRP 0.005 0.001 TRP A 64 HIS 0.002 0.001 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4146) covalent geometry : angle 0.52641 ( 5618) hydrogen bonds : bond 0.03195 ( 310) hydrogen bonds : angle 3.70953 ( 924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1201.11 seconds wall clock time: 21 minutes 8.62 seconds (1268.62 seconds total)