Starting phenix.real_space_refine on Fri Aug 22 14:39:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8do2_27588/08_2025/8do2_27588_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8do2_27588/08_2025/8do2_27588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8do2_27588/08_2025/8do2_27588_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8do2_27588/08_2025/8do2_27588_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8do2_27588/08_2025/8do2_27588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8do2_27588/08_2025/8do2_27588.map" } resolution = 2.95 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= 0.049 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 28 5.16 5 C 2803 2.51 5 N 674 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4226 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 480 Classifications: {'peptide': 61} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 57} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 244 Classifications: {'peptide': 31} Link IDs: {'PTRANS': 2, 'TRANS': 28} Chain: "A" Number of atoms: 3462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3462 Classifications: {'peptide': 449} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 18, 'TRANS': 430} Chain breaks: 2 Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 40 Unusual residues: {'SXU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.93, per 1000 atoms: 0.22 Number of scatterers: 4226 At special positions: 0 Unit cell: (85.05, 76.65, 79.8, 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 28 16.00 O 721 8.00 N 674 7.00 C 2803 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: 0.25 Conformation dependent library (CDL) restraints added in 160.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 992 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 4 sheets defined 74.5% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 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 95 Processing helix chain 'A' and resid 9 through 14 Processing helix chain 'A' and resid 27 through 47 Processing helix chain 'A' and resid 62 through 66 Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 108 through 134 Processing helix chain 'A' and resid 139 through 171 removed outlier: 5.903A pdb=" N ALA A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLY A 146 " --> pdb=" O GLU A 142 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ILE A 147 " --> pdb=" O MET A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 197 Processing helix chain 'A' and resid 211 through 223 Processing helix chain 'A' and resid 225 through 235 Processing helix chain 'A' and resid 241 through 260 removed outlier: 3.752A 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 315 through 322 Processing helix chain 'A' and resid 340 through 345 removed outlier: 3.547A pdb=" N TYR A 344 " --> pdb=" O GLY A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 357 Processing helix chain 'A' and resid 357 through 383 removed outlier: 3.617A pdb=" N ALA A 361 " --> pdb=" O ASP A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 398 Processing helix chain 'A' and resid 408 through 438 Proline residue: A 418 - end of helix Processing helix chain 'A' and resid 442 through 468 Processing sheet with id=AA1, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 265 Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 269 Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324 removed outlier: 6.470A pdb=" N THR A 323 " --> pdb=" O VAL A 338 " (cutoff:3.500A) 316 hydrogen bonds defined for protein. 939 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: 0.45 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 943 1.33 - 1.46: 1358 1.46 - 1.59: 1970 1.59 - 1.72: 0 1.72 - 1.85: 47 Bond restraints: 4318 Sorted by residual: bond pdb=" C22 SXU A 501 " pdb=" S20 SXU A 501 " ideal model delta sigma weight residual 1.759 1.852 -0.093 2.00e-02 2.50e+03 2.19e+01 bond pdb=" N03 SXU A 501 " pdb=" S02 SXU A 501 " ideal model delta sigma weight residual 1.648 1.737 -0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" C33 SXU A 501 " pdb=" S02 SXU A 501 " ideal model delta sigma weight residual 1.768 1.852 -0.084 2.00e-02 2.50e+03 1.76e+01 bond pdb=" N19 SXU A 501 " pdb=" S20 SXU A 501 " ideal model delta sigma weight residual 1.661 1.740 -0.079 2.00e-02 2.50e+03 1.54e+01 bond pdb=" C09 SXU A 501 " pdb=" C10 SXU A 501 " ideal model delta sigma weight residual 1.509 1.568 -0.059 2.00e-02 2.50e+03 8.72e+00 ... (remaining 4313 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.67: 5838 4.67 - 9.34: 8 9.34 - 14.01: 2 14.01 - 18.68: 1 18.68 - 23.36: 1 Bond angle restraints: 5850 Sorted by residual: angle pdb=" O21 SXU A 501 " pdb=" S20 SXU A 501 " pdb=" O29 SXU A 501 " ideal model delta sigma weight residual 117.02 93.66 23.36 3.00e+00 1.11e-01 6.06e+01 angle pdb=" O01 SXU A 501 " pdb=" S02 SXU A 501 " pdb=" O40 SXU A 501 " ideal model delta sigma weight residual 119.05 101.62 17.43 3.00e+00 1.11e-01 3.37e+01 angle pdb=" C04 SXU A 501 " pdb=" N03 SXU A 501 " pdb=" C05 SXU A 501 " ideal model delta sigma weight residual 115.30 125.30 -10.00 3.00e+00 1.11e-01 1.11e+01 angle pdb=" N GLY A 176 " pdb=" CA GLY A 176 " pdb=" C GLY A 176 " ideal model delta sigma weight residual 110.20 114.45 -4.25 1.32e+00 5.74e-01 1.04e+01 angle pdb=" N ARG A 223 " pdb=" CA ARG A 223 " pdb=" C ARG A 223 " ideal model delta sigma weight residual 110.23 114.84 -4.61 1.45e+00 4.76e-01 1.01e+01 ... (remaining 5845 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 2361 17.18 - 34.35: 185 34.35 - 51.53: 22 51.53 - 68.71: 4 68.71 - 85.88: 4 Dihedral angle restraints: 2576 sinusoidal: 1030 harmonic: 1546 Sorted by residual: 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 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" N ARG B 20 " pdb=" CA ARG B 20 " pdb=" CB ARG B 20 " pdb=" CG ARG B 20 " ideal model delta sinusoidal sigma weight residual 60.00 113.15 -53.15 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" CB MET B 47 " pdb=" CG MET B 47 " pdb=" SD MET B 47 " pdb=" CE MET B 47 " ideal model delta sinusoidal sigma weight residual -60.00 -108.15 48.15 3 1.50e+01 4.44e-03 8.60e+00 ... (remaining 2573 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 402 0.029 - 0.057: 174 0.057 - 0.085: 80 0.085 - 0.114: 22 0.114 - 0.142: 10 Chirality restraints: 688 Sorted by residual: chirality pdb=" CB VAL A 14 " pdb=" CA VAL A 14 " pdb=" CG1 VAL A 14 " pdb=" CG2 VAL A 14 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.07e-01 chirality pdb=" CB ILE A 123 " pdb=" CA ILE A 123 " pdb=" CG1 ILE A 123 " pdb=" CG2 ILE A 123 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.90e-01 chirality pdb=" CA ASN A 288 " pdb=" N ASN A 288 " pdb=" C ASN A 288 " pdb=" CB ASN A 288 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.75e-01 ... (remaining 685 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 239 " 0.033 5.00e-02 4.00e+02 4.94e-02 3.91e+00 pdb=" N PRO A 240 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO A 240 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 240 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 82 " -0.031 5.00e-02 4.00e+02 4.76e-02 3.62e+00 pdb=" N PRO A 83 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 83 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 83 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C22 SXU A 501 " 0.010 2.00e-02 2.50e+03 9.64e-03 1.86e+00 pdb=" C23 SXU A 501 " 0.000 2.00e-02 2.50e+03 pdb=" C24 SXU A 501 " 0.012 2.00e-02 2.50e+03 pdb=" C25 SXU A 501 " -0.006 2.00e-02 2.50e+03 pdb=" C26 SXU A 501 " -0.010 2.00e-02 2.50e+03 pdb=" C27 SXU A 501 " -0.000 2.00e-02 2.50e+03 pdb=" C28 SXU A 501 " 0.011 2.00e-02 2.50e+03 pdb=" S20 SXU A 501 " -0.016 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 950 2.78 - 3.31: 4236 3.31 - 3.84: 7269 3.84 - 4.37: 8081 4.37 - 4.90: 14578 Nonbonded interactions: 35114 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OG SER A 346 " model vdw 2.254 3.040 nonbonded pdb=" O ARG A 236 " pdb=" ND2 ASN A 241 " model vdw 2.261 3.120 nonbonded pdb=" O TYR A 131 " pdb=" OG1 THR A 134 " model vdw 2.362 3.040 nonbonded pdb=" O LEU A 181 " pdb=" OG1 THR A 185 " model vdw 2.372 3.040 nonbonded pdb=" OH TYR A 364 " pdb=" OD2 ASP A 436 " model vdw 2.394 3.040 ... (remaining 35109 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: 1.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.380 Find NCS groups from input model: 0.020 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:5.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.005 0.093 4318 Z= 0.250 Angle : 0.735 23.356 5850 Z= 0.348 Chirality : 0.040 0.142 688 Planarity : 0.004 0.049 711 Dihedral : 12.560 85.884 1584 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.22 % Allowed : 0.00 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.17 (0.37), residues: 531 helix: 2.26 (0.26), residues: 398 sheet: -3.75 (0.84), residues: 20 loop : -0.55 (0.63), residues: 113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 24 TYR 0.008 0.001 TYR A 457 PHE 0.010 0.001 PHE B 52 TRP 0.007 0.001 TRP A 64 HIS 0.002 0.001 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00489 ( 4318) covalent geometry : angle 0.73474 ( 5850) hydrogen bonds : bond 0.10057 ( 316) hydrogen bonds : angle 4.83414 ( 939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.153 Fit side-chains REVERT: B 30 ARG cc_start: 0.7222 (ttt90) cc_final: 0.6850 (mmt180) REVERT: A 294 GLN cc_start: 0.7923 (tm-30) cc_final: 0.7483 (tm-30) REVERT: A 368 MET cc_start: 0.7431 (tpp) cc_final: 0.7038 (tpp) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.7136 time to fit residues: 43.2489 Evaluate side-chains 43 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.1980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 50 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN ** A 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145946 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.116286 restraints weight = 4636.435| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.72 r_work: 0.3174 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7478 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4318 Z= 0.139 Angle : 0.542 7.683 5850 Z= 0.267 Chirality : 0.039 0.159 688 Planarity : 0.004 0.049 711 Dihedral : 5.748 54.788 625 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.55 % Allowed : 6.42 % Favored : 92.04 % 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 aren not related in a simple way. whole: 2.50 (0.37), residues: 531 helix: 2.47 (0.25), residues: 400 sheet: -3.57 (0.84), residues: 22 loop : -0.30 (0.64), residues: 109 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 228 TYR 0.004 0.001 TYR A 263 PHE 0.006 0.001 PHE B 49 TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4318) covalent geometry : angle 0.54244 ( 5850) hydrogen bonds : bond 0.03676 ( 316) hydrogen bonds : angle 4.21464 ( 939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.165 Fit side-chains REVERT: B 30 ARG cc_start: 0.7117 (ttt90) cc_final: 0.6096 (mmp-170) REVERT: B 66 VAL cc_start: 0.7584 (t) cc_final: 0.7346 (m) REVERT: A 167 GLU cc_start: 0.8230 (mt-10) cc_final: 0.7886 (mt-10) REVERT: A 189 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.7275 (tt0) REVERT: A 231 ARG cc_start: 0.6805 (ttm-80) cc_final: 0.5612 (mmp-170) REVERT: A 294 GLN cc_start: 0.8087 (tm-30) cc_final: 0.7706 (tm-30) REVERT: A 317 LEU cc_start: 0.8057 (mm) cc_final: 0.7338 (tp) outliers start: 7 outliers final: 1 residues processed: 58 average time/residue: 0.6190 time to fit residues: 36.9810 Evaluate side-chains 53 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 51 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 320 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 5 optimal weight: 0.9980 chunk 40 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 GLN A 241 ASN A 244 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.144289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.114753 restraints weight = 4634.712| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.72 r_work: 0.3121 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.1124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4318 Z= 0.151 Angle : 0.532 6.711 5850 Z= 0.263 Chirality : 0.039 0.156 688 Planarity : 0.004 0.050 711 Dihedral : 4.893 29.186 621 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.43 % Allowed : 8.41 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.52 (0.37), residues: 531 helix: 2.50 (0.25), residues: 400 sheet: -3.85 (0.77), residues: 20 loop : -0.36 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 228 TYR 0.005 0.001 TYR A 173 PHE 0.011 0.001 PHE A 261 TRP 0.009 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 4318) covalent geometry : angle 0.53179 ( 5850) hydrogen bonds : bond 0.03708 ( 316) hydrogen bonds : angle 4.18405 ( 939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.148 Fit side-chains REVERT: B 20 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6401 (ttp80) REVERT: B 30 ARG cc_start: 0.7136 (ttt90) cc_final: 0.6150 (mmp-170) REVERT: A 136 MET cc_start: 0.8373 (OUTLIER) cc_final: 0.8101 (ttp) REVERT: A 167 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7927 (mt-10) REVERT: A 189 GLU cc_start: 0.7719 (OUTLIER) cc_final: 0.7393 (tt0) REVERT: A 231 ARG cc_start: 0.6819 (ttm-80) cc_final: 0.5614 (mmp-170) REVERT: A 317 LEU cc_start: 0.8105 (mm) cc_final: 0.7375 (tp) outliers start: 11 outliers final: 0 residues processed: 58 average time/residue: 0.5539 time to fit residues: 33.1628 Evaluate side-chains 52 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain A residue 136 MET Chi-restraints excluded: chain A residue 189 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 41 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.148360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.117215 restraints weight = 4526.645| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 1.87 r_work: 0.3175 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4318 Z= 0.149 Angle : 0.535 6.659 5850 Z= 0.263 Chirality : 0.039 0.154 688 Planarity : 0.004 0.049 711 Dihedral : 4.705 25.700 621 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.33 % Allowed : 10.84 % Favored : 87.83 % 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 aren not related in a simple way. whole: 2.58 (0.37), residues: 531 helix: 2.55 (0.25), residues: 399 sheet: -3.60 (0.78), residues: 22 loop : -0.30 (0.62), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.004 0.001 TYR A 173 PHE 0.010 0.001 PHE A 261 TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 4318) covalent geometry : angle 0.53543 ( 5850) hydrogen bonds : bond 0.03624 ( 316) hydrogen bonds : angle 4.15693 ( 939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.153 Fit side-chains REVERT: B 20 ARG cc_start: 0.7728 (OUTLIER) cc_final: 0.6813 (ttp80) REVERT: B 30 ARG cc_start: 0.7417 (ttt90) cc_final: 0.6377 (mmp-170) REVERT: A 167 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8303 (mt-10) REVERT: A 189 GLU cc_start: 0.8147 (OUTLIER) cc_final: 0.7860 (tt0) REVERT: A 231 ARG cc_start: 0.7242 (ttm-80) cc_final: 0.6099 (mmp-170) REVERT: A 294 GLN cc_start: 0.8381 (tm-30) cc_final: 0.7909 (tt0) REVERT: A 317 LEU cc_start: 0.8288 (mm) cc_final: 0.7538 (tp) outliers start: 6 outliers final: 1 residues processed: 55 average time/residue: 0.5448 time to fit residues: 31.0297 Evaluate side-chains 53 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 189 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 22 optimal weight: 2.9990 chunk 47 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 48 optimal weight: 0.3980 chunk 1 optimal weight: 0.0370 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 = 0.3721 r_free = 0.3721 target = 0.148318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.118210 restraints weight = 4550.655| |-----------------------------------------------------------------------------| r_work (start): 0.3394 rms_B_bonded: 1.77 r_work: 0.3240 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4318 Z= 0.111 Angle : 0.504 6.349 5850 Z= 0.247 Chirality : 0.038 0.150 688 Planarity : 0.004 0.047 711 Dihedral : 4.476 21.953 621 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.33 % Allowed : 11.73 % Favored : 86.95 % 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 aren not related in a simple way. whole: 2.86 (0.37), residues: 531 helix: 2.81 (0.25), residues: 393 sheet: -3.39 (0.82), residues: 22 loop : -0.30 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 273 TYR 0.005 0.001 TYR A 131 PHE 0.007 0.001 PHE A 261 TRP 0.007 0.001 TRP A 64 HIS 0.001 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 4318) covalent geometry : angle 0.50376 ( 5850) hydrogen bonds : bond 0.03345 ( 316) hydrogen bonds : angle 4.06893 ( 939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.096 Fit side-chains REVERT: B 30 ARG cc_start: 0.7495 (ttt90) cc_final: 0.6440 (mmp-170) REVERT: A 23 GLU cc_start: 0.7099 (pm20) cc_final: 0.6243 (tt0) REVERT: A 167 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8288 (mt-10) REVERT: A 189 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7814 (tt0) REVERT: A 317 LEU cc_start: 0.8329 (mm) cc_final: 0.7779 (tt) outliers start: 6 outliers final: 1 residues processed: 54 average time/residue: 0.4842 time to fit residues: 27.1718 Evaluate side-chains 51 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 49 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 189 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 43 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 41 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3691 r_free = 0.3691 target = 0.146068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.115871 restraints weight = 4681.471| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.78 r_work: 0.3208 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4318 Z= 0.150 Angle : 0.529 6.365 5850 Z= 0.260 Chirality : 0.039 0.150 688 Planarity : 0.004 0.048 711 Dihedral : 4.582 24.310 621 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.55 % Allowed : 12.39 % Favored : 86.06 % 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 aren not related in a simple way. whole: 2.78 (0.37), residues: 531 helix: 2.76 (0.25), residues: 393 sheet: -3.49 (0.80), residues: 22 loop : -0.34 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.006 0.001 TYR A 302 PHE 0.009 0.001 PHE A 261 TRP 0.008 0.001 TRP A 64 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 4318) covalent geometry : angle 0.52882 ( 5850) hydrogen bonds : bond 0.03601 ( 316) hydrogen bonds : angle 4.12856 ( 939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.097 Fit side-chains REVERT: B 20 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.6807 (ttp80) REVERT: B 30 ARG cc_start: 0.7449 (ttt90) cc_final: 0.6404 (mmp-170) REVERT: A 23 GLU cc_start: 0.7077 (pm20) cc_final: 0.6184 (tt0) REVERT: A 167 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8299 (mt-10) REVERT: A 189 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.7830 (tt0) REVERT: A 294 GLN cc_start: 0.8268 (tm-30) cc_final: 0.7855 (tt0) REVERT: A 317 LEU cc_start: 0.8287 (mm) cc_final: 0.7758 (tt) outliers start: 7 outliers final: 4 residues processed: 54 average time/residue: 0.5264 time to fit residues: 29.3914 Evaluate side-chains 55 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 368 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 34 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 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 = 0.3723 r_free = 0.3723 target = 0.148568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.117694 restraints weight = 4671.711| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.88 r_work: 0.3198 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4318 Z= 0.142 Angle : 0.518 6.534 5850 Z= 0.255 Chirality : 0.039 0.150 688 Planarity : 0.004 0.048 711 Dihedral : 4.757 26.299 621 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.77 % Allowed : 12.17 % Favored : 86.06 % 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 aren not related in a simple way. whole: 2.76 (0.37), residues: 531 helix: 2.74 (0.25), residues: 393 sheet: -3.60 (0.78), residues: 22 loop : -0.33 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 273 TYR 0.007 0.001 TYR A 302 PHE 0.008 0.001 PHE A 261 TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4318) covalent geometry : angle 0.51833 ( 5850) hydrogen bonds : bond 0.03549 ( 316) hydrogen bonds : angle 4.11287 ( 939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.155 Fit side-chains REVERT: B 20 ARG cc_start: 0.7753 (OUTLIER) cc_final: 0.6863 (ttp80) REVERT: B 30 ARG cc_start: 0.7485 (ttt90) cc_final: 0.6432 (mmp-170) REVERT: A 23 GLU cc_start: 0.7107 (pm20) cc_final: 0.6222 (tt0) REVERT: A 167 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8365 (mt-10) REVERT: A 189 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: A 294 GLN cc_start: 0.8308 (tm-30) cc_final: 0.7864 (tt0) REVERT: A 317 LEU cc_start: 0.8259 (mm) cc_final: 0.7740 (tt) outliers start: 8 outliers final: 4 residues processed: 56 average time/residue: 0.5640 time to fit residues: 32.6957 Evaluate side-chains 55 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 368 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 50 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.149685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.118970 restraints weight = 4536.005| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.84 r_work: 0.3217 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4318 Z= 0.120 Angle : 0.504 6.765 5850 Z= 0.247 Chirality : 0.038 0.149 688 Planarity : 0.004 0.047 711 Dihedral : 4.761 28.752 621 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.33 % Allowed : 13.72 % Favored : 84.96 % 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 aren not related in a simple way. whole: 2.81 (0.37), residues: 531 helix: 2.79 (0.25), residues: 393 sheet: -3.51 (0.80), residues: 22 loop : -0.35 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 273 TYR 0.008 0.001 TYR A 302 PHE 0.007 0.001 PHE A 261 TRP 0.008 0.001 TRP A 64 HIS 0.002 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 4318) covalent geometry : angle 0.50376 ( 5850) hydrogen bonds : bond 0.03420 ( 316) hydrogen bonds : angle 4.08059 ( 939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.157 Fit side-chains REVERT: B 20 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.6894 (ttp80) REVERT: B 30 ARG cc_start: 0.7453 (ttt90) cc_final: 0.6430 (mmp-170) REVERT: A 23 GLU cc_start: 0.6997 (pm20) cc_final: 0.6172 (tt0) REVERT: A 167 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8374 (mt-10) REVERT: A 189 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: A 294 GLN cc_start: 0.8273 (tm-30) cc_final: 0.7839 (tt0) REVERT: A 317 LEU cc_start: 0.8337 (mm) cc_final: 0.7812 (tt) outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.5652 time to fit residues: 31.0704 Evaluate side-chains 55 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 20 ARG Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 189 GLU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 368 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 41 optimal weight: 0.2980 chunk 2 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 10 optimal weight: 0.0770 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 28 optimal weight: 2.9990 chunk 42 optimal weight: 0.0980 overall best weight: 0.1316 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.151681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.121663 restraints weight = 4590.745| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 1.78 r_work: 0.3287 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4318 Z= 0.091 Angle : 0.471 7.783 5850 Z= 0.231 Chirality : 0.037 0.146 688 Planarity : 0.004 0.045 711 Dihedral : 4.498 28.043 621 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.11 % Allowed : 14.16 % Favored : 84.73 % 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 aren not related in a simple way. whole: 3.02 (0.37), residues: 531 helix: 2.95 (0.25), residues: 393 sheet: -3.44 (0.87), residues: 20 loop : -0.37 (0.57), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.007 0.001 TYR A 302 PHE 0.006 0.001 PHE B 44 TRP 0.005 0.001 TRP A 64 HIS 0.001 0.000 HIS B 58 Details of bonding type rmsd covalent geometry : bond 0.00188 ( 4318) covalent geometry : angle 0.47083 ( 5850) hydrogen bonds : bond 0.03074 ( 316) hydrogen bonds : angle 3.94874 ( 939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.097 Fit side-chains REVERT: B 30 ARG cc_start: 0.7348 (ttt90) cc_final: 0.6340 (mmp-170) REVERT: A 23 GLU cc_start: 0.7066 (pm20) cc_final: 0.6091 (tt0) REVERT: A 167 GLU cc_start: 0.8635 (mt-10) cc_final: 0.8420 (mt-10) REVERT: A 273 ARG cc_start: 0.7084 (mtt90) cc_final: 0.6763 (mpt180) REVERT: A 294 GLN cc_start: 0.8130 (tm-30) cc_final: 0.7763 (tt0) REVERT: A 317 LEU cc_start: 0.8296 (mm) cc_final: 0.7771 (tt) outliers start: 5 outliers final: 3 residues processed: 56 average time/residue: 0.5247 time to fit residues: 30.4198 Evaluate side-chains 49 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.0040 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 43 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 275 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.147463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.117582 restraints weight = 4551.303| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.75 r_work: 0.3232 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4318 Z= 0.140 Angle : 0.520 8.507 5850 Z= 0.255 Chirality : 0.039 0.148 688 Planarity : 0.004 0.046 711 Dihedral : 4.667 29.200 621 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.33 % Allowed : 15.04 % Favored : 83.63 % 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 aren not related in a simple way. whole: 2.90 (0.37), residues: 531 helix: 2.85 (0.25), residues: 393 sheet: -3.39 (0.85), residues: 22 loop : -0.31 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.012 0.001 TYR A 302 PHE 0.009 0.001 PHE A 261 TRP 0.006 0.001 TRP A 34 HIS 0.003 0.001 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4318) covalent geometry : angle 0.51978 ( 5850) hydrogen bonds : bond 0.03472 ( 316) hydrogen bonds : angle 4.07651 ( 939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1062 Ramachandran restraints generated. 531 Oldfield, 0 Emsley, 531 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.169 Fit side-chains REVERT: B 30 ARG cc_start: 0.7352 (ttt90) cc_final: 0.6415 (mmp-170) REVERT: A 216 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7275 (tp) REVERT: A 294 GLN cc_start: 0.8240 (tm-30) cc_final: 0.7865 (tt0) REVERT: A 317 LEU cc_start: 0.8300 (mm) cc_final: 0.7779 (tt) outliers start: 6 outliers final: 4 residues processed: 50 average time/residue: 0.5009 time to fit residues: 26.0259 Evaluate side-chains 52 residues out of total 460 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain A residue 216 LEU Chi-restraints excluded: chain A residue 272 VAL Chi-restraints excluded: chain A residue 278 ILE Chi-restraints excluded: chain A residue 368 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 27 optimal weight: 0.3980 chunk 10 optimal weight: 0.0670 chunk 43 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4718 ------------------------------------------------------------------------------- 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 = 0.3736 r_free = 0.3736 target = 0.150022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.119175 restraints weight = 4576.229| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.87 r_work: 0.3179 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4318 Z= 0.122 Angle : 0.520 8.690 5850 Z= 0.254 Chirality : 0.039 0.148 688 Planarity : 0.004 0.046 711 Dihedral : 4.684 30.047 621 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.55 % Allowed : 15.71 % Favored : 82.74 % 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 aren not related in a simple way. whole: 2.89 (0.37), residues: 531 helix: 2.83 (0.25), residues: 393 sheet: -3.29 (0.87), residues: 22 loop : -0.31 (0.59), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 273 TYR 0.013 0.001 TYR A 302 PHE 0.007 0.001 PHE A 312 TRP 0.007 0.001 TRP A 64 HIS 0.002 0.000 HIS A 360 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4318) covalent geometry : angle 0.51969 ( 5850) hydrogen bonds : bond 0.03346 ( 316) hydrogen bonds : angle 4.03968 ( 939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1383.63 seconds wall clock time: 24 minutes 16.58 seconds (1456.58 seconds total)