Starting phenix.real_space_refine on Fri Sep 11 00:15:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6b19_7031/09_2026/6b19_7031.cif Found real_map, /net/cci-nas-00/data/ceres_data/6b19_7031/09_2026/6b19_7031.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6b19_7031/09_2026/6b19_7031.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6b19_7031/09_2026/6b19_7031.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6b19_7031/09_2026/6b19_7031.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6b19_7031/09_2026/6b19_7031.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6b19_7031/09_2026/6b19_7031.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6b19_7031/09_2026/6b19_7031.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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: 5 Type Number sf(0) Gaussians P 37 5.49 5 C 3032 2.51 5 N 1054 2.21 5 O 1167 1.98 5 H 409 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5699 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 2512 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 456} Link IDs: {'CIS': 1, 'PTRANS': 33, 'TRANS': 473} Chain breaks: 11 Unresolved chain link angles: 33 Unresolved non-hydrogen bonds: 1751 Unresolved non-hydrogen angles: 2259 Unresolved non-hydrogen dihedrals: 1501 Unresolved non-hydrogen chiralities: 154 Planarities with less than four sites: {'GLU:plan': 42, 'GLN:plan1': 34, 'TRP:plan': 17, 'ASN:plan1': 18, 'TYR:plan': 22, 'PHE:plan': 12, 'ARG:plan': 15, 'ASP:plan': 21, 'HIS:plan': 8} Unresolved non-hydrogen planarities: 915 Chain: "B" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 399, 1974 Classifications: {'peptide': 399} Incomplete info: {'truncation_to_alanine': 363} Link IDs: {'PTRANS': 28, 'TRANS': 370} Chain breaks: 7 Unresolved chain link angles: 28 Unresolved non-hydrogen bonds: 1417 Unresolved non-hydrogen angles: 1829 Unresolved non-hydrogen dihedrals: 1227 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'GLU:plan': 35, 'ASP:plan': 18, 'GLN:plan1': 24, 'TRP:plan': 16, 'ASN:plan1': 12, 'PHE:plan': 11, 'ARG:plan': 13, 'HIS:plan': 6, 'TYR:plan': 16} Unresolved non-hydrogen planarities: 743 Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 612 Classifications: {'RNAv2': 19} Modifications used: {'rna3p_pur': 11, 'rna3p_pyr': 7} Link IDs: {'rna3p': 18} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 601 Classifications: {'DNA': 2, 'RNAv2': 17} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 11} Link IDs: {'rna3p': 18} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.47, per 1000 atoms: 0.26 Number of scatterers: 5699 At special positions: 0 Unit cell: (96, 110, 91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) P 37 15.00 O 1167 8.00 N 1054 7.00 C 3032 6.00 H 409 1.00 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: 0.62 Conformation dependent library (CDL) restraints added in 374.7 milliseconds 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1716 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 37.3% alpha, 5.4% beta 19 base pairs and 16 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 33 through 44 removed outlier: 4.276A pdb=" N THR A 39 " --> pdb=" O VAL A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 83 Processing helix chain 'A' and resid 155 through 175 removed outlier: 3.617A pdb=" N ILE A 159 " --> pdb=" O GLY A 155 " (cutoff:3.500A) Proline residue: A 170 - end of helix Processing helix chain 'A' and resid 196 through 211 removed outlier: 3.633A pdb=" N LYS A 201 " --> pdb=" O GLN A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 268 Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 276 through 283 removed outlier: 4.006A pdb=" N LEU A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 312 removed outlier: 3.520A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS A 311 " --> pdb=" O ARG A 307 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N GLU A 312 " --> pdb=" O GLU A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 383 Processing helix chain 'A' and resid 394 through 403 Processing helix chain 'A' and resid 473 through 489 removed outlier: 3.699A pdb=" N ASP A 488 " --> pdb=" O LEU A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 508 removed outlier: 3.946A pdb=" N LEU A 503 " --> pdb=" O SER A 499 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ALA A 508 " --> pdb=" O GLY A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 528 Processing helix chain 'A' and resid 545 through 550 Processing helix chain 'B' and resid 28 through 45 removed outlier: 3.680A pdb=" N VAL B 35 " --> pdb=" O ILE B 31 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N GLU B 36 " --> pdb=" O LYS B 32 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 84 Processing helix chain 'B' and resid 84 through 92 removed outlier: 4.035A pdb=" N TRP B 88 " --> pdb=" O THR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 118 Processing helix chain 'B' and resid 122 through 126 removed outlier: 4.003A pdb=" N LYS B 126 " --> pdb=" O ASP B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 138 Processing helix chain 'B' and resid 154 through 160 Processing helix chain 'B' and resid 160 through 175 Proline residue: B 170 - end of helix Processing helix chain 'B' and resid 194 through 212 Processing helix chain 'B' and resid 253 through 268 Processing helix chain 'B' and resid 278 through 283 Processing helix chain 'B' and resid 296 through 312 Processing helix chain 'B' and resid 363 through 384 Processing helix chain 'B' and resid 394 through 402 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 180 removed outlier: 3.545A pdb=" N VAL A 179 " --> pdb=" O GLY A 190 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 350 through 353 removed outlier: 4.936A pdb=" N GLN A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU A 328 " --> pdb=" O GLN A 340 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N ILE A 329 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N PHE A 389 " --> pdb=" O GLU A 415 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 441 through 443 Processing sheet with id=AA5, first strand: chain 'A' and resid 492 through 493 Processing sheet with id=AA6, first strand: chain 'B' and resid 61 through 63 Processing sheet with id=AA7, first strand: chain 'B' and resid 181 through 183 Processing sheet with id=AA8, first strand: chain 'B' and resid 327 through 330 removed outlier: 6.634A pdb=" N ILE B 341 " --> pdb=" O LEU B 349 " (cutoff:3.500A) 246 hydrogen bonds defined for protein. 690 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 52 hydrogen bonds 104 hydrogen bond angles 0 basepair planarities 19 basepair parallelities 16 stacking parallelities Total time for adding SS restraints: 0.91 Time building geometry restraints manager: 0.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.75 - 1.20: 409 1.20 - 1.64: 5362 1.64 - 2.09: 0 2.09 - 2.53: 0 2.53 - 2.98: 1 Bond restraints: 5772 Sorted by residual: bond pdb=" C THR A 286 " pdb=" N LEU A 289 " ideal model delta sigma weight residual 1.329 2.978 -1.649 1.40e-02 5.10e+03 1.39e+04 bond pdb=" N6 A C 191 " pdb=" H61 A C 191 " ideal model delta sigma weight residual 0.860 0.751 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" N6 A C 191 " pdb=" H62 A C 191 " ideal model delta sigma weight residual 0.860 0.925 -0.065 2.00e-02 2.50e+03 1.05e+01 bond pdb=" C5 DG D 71 " pdb=" C6 DG D 71 " ideal model delta sigma weight residual 1.419 1.395 0.024 1.00e-02 1.00e+04 5.63e+00 bond pdb=" C4' DC D 77 " pdb=" C3' DC D 77 " ideal model delta sigma weight residual 1.529 1.507 0.022 1.00e-02 1.00e+04 4.95e+00 ... (remaining 5767 not shown) Histogram of bond angle deviations from ideal: 0.00 - 16.28: 8510 16.28 - 32.56: 0 32.56 - 48.84: 1 48.84 - 65.12: 0 65.12 - 81.40: 1 Bond angle restraints: 8512 Sorted by residual: angle pdb=" O THR A 286 " pdb=" C THR A 286 " pdb=" N LEU A 289 " ideal model delta sigma weight residual 122.59 41.19 81.40 1.33e+00 5.65e-01 3.75e+03 angle pdb=" CA THR A 286 " pdb=" C THR A 286 " pdb=" N LEU A 289 " ideal model delta sigma weight residual 116.84 152.89 -36.05 1.71e+00 3.42e-01 4.45e+02 angle pdb=" C ASN A 54 " pdb=" N PRO A 55 " pdb=" CA PRO A 55 " ideal model delta sigma weight residual 119.84 128.00 -8.16 1.25e+00 6.40e-01 4.26e+01 angle pdb=" O5' DG D 71 " pdb=" C5' DG D 71 " pdb=" C4' DG D 71 " ideal model delta sigma weight residual 109.40 112.80 -3.40 8.00e-01 1.56e+00 1.80e+01 angle pdb=" C THR A 397 " pdb=" N TRP A 398 " pdb=" CA TRP A 398 " ideal model delta sigma weight residual 120.29 114.26 6.03 1.42e+00 4.96e-01 1.80e+01 ... (remaining 8507 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.31: 3047 29.31 - 58.62: 47 58.62 - 87.93: 10 87.93 - 117.24: 2 117.24 - 146.55: 2 Dihedral angle restraints: 3108 sinusoidal: 505 harmonic: 2603 Sorted by residual: dihedral pdb=" O5' C C 185 " pdb=" C5' C C 185 " pdb=" C4' C C 185 " pdb=" C3' C C 185 " ideal model delta sinusoidal sigma weight residual 60.00 35.75 24.25 3 6.40e+00 2.44e-02 1.83e+01 dihedral pdb=" CA GLU A 413 " pdb=" C GLU A 413 " pdb=" N TRP A 414 " pdb=" CA TRP A 414 " ideal model delta harmonic sigma weight residual -180.00 -160.37 -19.63 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASN B 418 " pdb=" C ASN B 418 " pdb=" N THR B 419 " pdb=" CA THR B 419 " ideal model delta harmonic sigma weight residual -180.00 -160.86 -19.14 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 3105 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 773 0.062 - 0.124: 221 0.124 - 0.186: 16 0.186 - 0.248: 27 0.248 - 0.310: 6 Chirality restraints: 1043 Sorted by residual: chirality pdb=" P G D 65 " pdb=" OP1 G D 65 " pdb=" OP2 G D 65 " pdb=" O5' G D 65 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" P G C 184 " pdb=" OP1 G C 184 " pdb=" OP2 G C 184 " pdb=" O5' G C 184 " both_signs ideal model delta sigma weight residual True 2.17 -2.44 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" P U C 182 " pdb=" OP1 U C 182 " pdb=" OP2 U C 182 " pdb=" O5' U C 182 " both_signs ideal model delta sigma weight residual True 2.17 -2.43 -0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 1040 not shown) Planarity restraints: 958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 286 " -0.201 2.00e-02 2.50e+03 1.73e-01 2.99e+02 pdb=" C THR A 286 " 0.240 2.00e-02 2.50e+03 pdb=" O THR A 286 " 0.082 2.00e-02 2.50e+03 pdb=" N LEU A 289 " -0.122 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 41 " 0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C MET A 41 " -0.062 2.00e-02 2.50e+03 pdb=" O MET A 41 " 0.023 2.00e-02 2.50e+03 pdb=" N GLU A 42 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 296 " -0.017 2.00e-02 2.50e+03 3.42e-02 1.17e+01 pdb=" C THR B 296 " 0.059 2.00e-02 2.50e+03 pdb=" O THR B 296 " -0.022 2.00e-02 2.50e+03 pdb=" N GLU B 297 " -0.020 2.00e-02 2.50e+03 ... (remaining 955 not shown) Histogram of nonbonded interaction distances: 1.78 - 2.34: 282 2.34 - 2.91: 4305 2.91 - 3.47: 8362 3.47 - 4.04: 11082 4.04 - 4.60: 14332 Nonbonded interactions: 38363 Sorted by model distance: nonbonded pdb=" H2' G D 69 " pdb=" H8 G D 70 " model vdw 1.781 2.270 nonbonded pdb=" H2' C D 72 " pdb=" H8 G D 73 " model vdw 1.806 2.270 nonbonded pdb=" H2' G C 186 " pdb=" H6 C C 187 " model vdw 1.839 2.270 nonbonded pdb=" H2' G D 73 " pdb=" H6 C D 74 " model vdw 1.853 2.270 nonbonded pdb=" H2' G C 183 " pdb=" H8 G C 184 " model vdw 1.863 2.270 ... (remaining 38358 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.070 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.670 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 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 : 0.023 1.649 5363 Z= 1.654 Angle : 1.423 81.401 7576 Z= 0.941 Chirality : 0.065 0.310 1043 Planarity : 0.008 0.173 925 Dihedral : 10.088 63.060 1323 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.12 % Allowed : 19.42 % Favored : 80.46 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.73 (0.22), residues: 865 helix: -2.49 (0.24), residues: 298 sheet: -3.46 (0.48), residues: 95 loop : -5.02 (0.21), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.02328 / 1.65 ( 5363) covalent geometry : angle 1.42286 / 0.94 ( 7576) hydrogen bonds : bond 0.16902 / 12.44 ( 298) hydrogen bonds : angle 8.80554 / 6.26 ( 794) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1730 Ramachandran restraints generated. 865 Oldfield, 0 Emsley, 865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.202 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0263 time to fit residues: 0.7250 Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 chunk 5 optimal weight: 40.0000 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 38 optimal weight: 30.0000 chunk 61 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 40.0000 overall best weight: 14.9996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.061798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.055257 restraints weight = 142201.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.055640 restraints weight = 117123.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.055939 restraints weight = 101201.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.056155 restraints weight = 90366.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.056329 restraints weight = 82695.381| |-----------------------------------------------------------------------------| r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6232 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 5363 Z= 0.430 Angle : 1.237 10.306 7576 Z= 0.634 Chirality : 0.063 0.323 1043 Planarity : 0.006 0.021 925 Dihedral : 12.089 72.247 1323 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 42.89 Ramachandran Plot: Outliers : 0.46 % Allowed : 26.53 % Favored : 73.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: -5.64 (0.23), residues: 867 helix: -2.33 (0.24), residues: 302 sheet: -3.61 (0.54), residues: 74 loop : -4.99 (0.21), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00708 / 0.43 ( 5363) covalent geometry : angle 1.23670 / 0.63 ( 7576) hydrogen bonds : bond 0.07672 / 5.72 ( 298) hydrogen bonds : angle 8.81449 / 6.19 ( 794) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.198 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0277 time to fit residues: 0.7964 Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 7 optimal weight: 50.0000 chunk 49 optimal weight: 30.0000 chunk 85 optimal weight: 30.0000 chunk 43 optimal weight: 30.0000 chunk 22 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 5 optimal weight: 30.0000 chunk 69 optimal weight: 5.9990 chunk 64 optimal weight: 30.0000 chunk 38 optimal weight: 7.9990 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.062296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.055915 restraints weight = 143137.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.056335 restraints weight = 116723.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.056651 restraints weight = 99416.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.056896 restraints weight = 88173.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.057062 restraints weight = 79889.767| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5363 Z= 0.244 Angle : 0.822 6.656 7576 Z= 0.418 Chirality : 0.054 0.219 1043 Planarity : 0.003 0.015 925 Dihedral : 11.022 72.002 1323 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 23.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.18 % Favored : 79.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.86 (0.24), residues: 867 helix: -1.28 (0.27), residues: 309 sheet: -3.64 (0.52), residues: 77 loop : -4.77 (0.22), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.24 ( 5363) covalent geometry : angle 0.82223 / 0.42 ( 7576) hydrogen bonds : bond 0.05716 / 4.21 ( 298) hydrogen bonds : angle 7.52658 / 5.29 ( 794) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.209 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0295 time to fit residues: 0.8336 Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 50 optimal weight: 40.0000 chunk 77 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 72 optimal weight: 40.0000 chunk 52 optimal weight: 40.0000 chunk 24 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 40.0000 chunk 29 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.063004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.056731 restraints weight = 144282.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.057179 restraints weight = 116867.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.057507 restraints weight = 99037.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.057744 restraints weight = 87440.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.057952 restraints weight = 79140.683| |-----------------------------------------------------------------------------| r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6245 moved from start: 0.3372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 5363 Z= 0.167 Angle : 0.676 5.587 7576 Z= 0.334 Chirality : 0.050 0.175 1043 Planarity : 0.002 0.016 925 Dihedral : 10.409 71.815 1323 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 18.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.76 % Favored : 79.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -3.85 (0.27), residues: 867 helix: 0.03 (0.29), residues: 314 sheet: -3.55 (0.54), residues: 79 loop : -4.48 (0.23), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.17 ( 5363) covalent geometry : angle 0.67628 / 0.33 ( 7576) hydrogen bonds : bond 0.04474 / 3.25 ( 298) hydrogen bonds : angle 6.46866 / 4.55 ( 794) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.240 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0302 time to fit residues: 0.9175 Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 34 optimal weight: 50.0000 chunk 76 optimal weight: 20.0000 chunk 37 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 30.0000 chunk 42 optimal weight: 40.0000 chunk 90 optimal weight: 9.9990 chunk 69 optimal weight: 30.0000 chunk 73 optimal weight: 10.0000 chunk 62 optimal weight: 20.0000 chunk 25 optimal weight: 30.0000 overall best weight: 10.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.060385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.054148 restraints weight = 145124.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.054556 restraints weight = 117767.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.054868 restraints weight = 100651.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.055104 restraints weight = 88824.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.055265 restraints weight = 80452.470| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6278 moved from start: 0.4367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 5363 Z= 0.313 Angle : 0.971 8.551 7576 Z= 0.486 Chirality : 0.056 0.251 1043 Planarity : 0.004 0.016 925 Dihedral : 11.621 74.563 1323 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 33.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.76 % Favored : 73.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.64 (0.25), residues: 867 helix: -0.99 (0.27), residues: 313 sheet: -2.71 (0.69), residues: 52 loop : -4.85 (0.22), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.31 ( 5363) covalent geometry : angle 0.97097 / 0.49 ( 7576) hydrogen bonds : bond 0.06542 / 4.82 ( 298) hydrogen bonds : angle 7.95677 / 5.55 ( 794) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0288 time to fit residues: 0.8328 Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 24 optimal weight: 2.9990 chunk 44 optimal weight: 9.9990 chunk 20 optimal weight: 20.0000 chunk 42 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 79 optimal weight: 40.0000 chunk 85 optimal weight: 30.0000 chunk 82 optimal weight: 30.0000 chunk 27 optimal weight: 40.0000 overall best weight: 7.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.061291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.055158 restraints weight = 143058.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.055580 restraints weight = 115957.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055903 restraints weight = 98726.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.056149 restraints weight = 86998.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.056335 restraints weight = 78650.570| |-----------------------------------------------------------------------------| r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6286 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 5363 Z= 0.216 Angle : 0.792 6.826 7576 Z= 0.392 Chirality : 0.052 0.207 1043 Planarity : 0.003 0.015 925 Dihedral : 11.127 74.392 1323 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 21.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.49 % Favored : 77.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.25 (0.26), residues: 867 helix: -0.57 (0.29), residues: 317 sheet: -3.31 (0.57), residues: 74 loop : -4.63 (0.23), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.22 ( 5363) covalent geometry : angle 0.79192 / 0.39 ( 7576) hydrogen bonds : bond 0.05284 / 3.84 ( 298) hydrogen bonds : angle 7.23900 / 5.06 ( 794) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.189 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0266 time to fit residues: 0.7840 Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 31 optimal weight: 50.0000 chunk 72 optimal weight: 40.0000 chunk 83 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 25 optimal weight: 50.0000 chunk 80 optimal weight: 50.0000 chunk 47 optimal weight: 10.0000 chunk 76 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 79 optimal weight: 40.0000 overall best weight: 14.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.059348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.052978 restraints weight = 144488.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.053321 restraints weight = 118047.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.053639 restraints weight = 102044.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.053863 restraints weight = 90668.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.054035 restraints weight = 82451.474| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6297 moved from start: 0.5585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 5363 Z= 0.391 Angle : 1.176 10.719 7576 Z= 0.590 Chirality : 0.061 0.277 1043 Planarity : 0.005 0.018 925 Dihedral : 12.749 78.503 1323 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 43.15 Ramachandran Plot: Outliers : 0.46 % Allowed : 32.64 % Favored : 66.90 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.24 % 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: -5.43 (0.24), residues: 867 helix: -1.91 (0.26), residues: 303 sheet: -3.87 (0.53), residues: 79 loop : -4.98 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00657 / 0.39 ( 5363) covalent geometry : angle 1.17644 / 0.59 ( 7576) hydrogen bonds : bond 0.07975 / 5.86 ( 298) hydrogen bonds : angle 9.05443 / 6.31 ( 794) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.202 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0244 time to fit residues: 0.7449 Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 34 optimal weight: 0.0060 chunk 19 optimal weight: 50.0000 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 62 optimal weight: 0.0020 chunk 12 optimal weight: 8.9990 chunk 42 optimal weight: 40.0000 chunk 36 optimal weight: 8.9990 chunk 35 optimal weight: 6.9990 overall best weight: 4.4010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.061522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055435 restraints weight = 142739.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.055847 restraints weight = 116851.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.056146 restraints weight = 99835.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.056388 restraints weight = 88284.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.056544 restraints weight = 80312.481| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6284 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5363 Z= 0.180 Angle : 0.768 6.950 7576 Z= 0.376 Chirality : 0.053 0.206 1043 Planarity : 0.002 0.013 925 Dihedral : 11.432 75.560 1323 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.76 % Favored : 82.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.35 (0.26), residues: 867 helix: -0.72 (0.28), residues: 315 sheet: -3.64 (0.54), residues: 80 loop : -4.56 (0.24), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.18 ( 5363) covalent geometry : angle 0.76786 / 0.38 ( 7576) hydrogen bonds : bond 0.05259 / 3.78 ( 298) hydrogen bonds : angle 7.21346 / 5.05 ( 794) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.194 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0291 time to fit residues: 0.8266 Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 chunk 33 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 74 optimal weight: 20.0000 chunk 84 optimal weight: 20.0000 chunk 46 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 30.0000 chunk 36 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 overall best weight: 6.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.060779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.054737 restraints weight = 143324.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.055144 restraints weight = 116551.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.055461 restraints weight = 99441.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.055701 restraints weight = 87529.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.055901 restraints weight = 79025.513| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.5508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5363 Z= 0.210 Angle : 0.795 7.124 7576 Z= 0.390 Chirality : 0.052 0.193 1043 Planarity : 0.003 0.014 925 Dihedral : 11.435 75.365 1323 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 23.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 28.49 % Favored : 71.51 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.28 (0.27), residues: 867 helix: -0.50 (0.29), residues: 310 sheet: -3.59 (0.55), residues: 79 loop : -4.60 (0.24), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.21 ( 5363) covalent geometry : angle 0.79520 / 0.39 ( 7576) hydrogen bonds : bond 0.05300 / 3.83 ( 298) hydrogen bonds : angle 7.27387 / 5.08 ( 794) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.189 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0282 time to fit residues: 0.7861 Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 88 optimal weight: 40.0000 chunk 2 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 4 optimal weight: 20.0000 chunk 12 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 20.0000 chunk 45 optimal weight: 40.0000 chunk 54 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 28 optimal weight: 8.9990 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.060949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.054928 restraints weight = 145496.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.055345 restraints weight = 118019.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.055672 restraints weight = 100556.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.055914 restraints weight = 88154.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.056091 restraints weight = 79659.136| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.5634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5363 Z= 0.195 Angle : 0.764 7.027 7576 Z= 0.373 Chirality : 0.052 0.182 1043 Planarity : 0.003 0.014 925 Dihedral : 11.336 74.819 1323 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.80 % Favored : 75.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % 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: -4.11 (0.27), residues: 867 helix: -0.30 (0.29), residues: 310 sheet: -3.15 (0.64), residues: 62 loop : -4.61 (0.24), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.19 ( 5363) covalent geometry : angle 0.76376 / 0.37 ( 7576) hydrogen bonds : bond 0.05120 / 3.69 ( 298) hydrogen bonds : angle 7.06841 / 4.93 ( 794) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.203 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0268 time to fit residues: 0.7740 Evaluate side-chains 10 residues out of total 819 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 3 optimal weight: 40.0000 chunk 54 optimal weight: 20.0000 chunk 23 optimal weight: 50.0000 chunk 11 optimal weight: 20.0000 chunk 76 optimal weight: 20.0000 chunk 41 optimal weight: 40.0000 chunk 19 optimal weight: 50.0000 chunk 51 optimal weight: 30.0000 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 0.0570 chunk 78 optimal weight: 30.0000 overall best weight: 12.6112 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.053224 restraints weight = 142443.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.053600 restraints weight = 116542.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.053895 restraints weight = 100071.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.054120 restraints weight = 88575.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.054300 restraints weight = 80244.458| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6321 moved from start: 0.6162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 5363 Z= 0.337 Angle : 1.026 8.669 7576 Z= 0.509 Chirality : 0.057 0.232 1043 Planarity : 0.004 0.016 925 Dihedral : 12.342 77.455 1323 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 34.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 31.83 % Favored : 68.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.12 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -4.89 (0.25), residues: 867 helix: -1.20 (0.28), residues: 298 sheet: -3.51 (0.62), residues: 60 loop : -4.82 (0.23), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 56 PHE 0.000 0.000 PHE A 61 TRP 0.000 0.000 TRP A 24 Details of bonding type rmsd/Z covalent geometry : bond 0.00565 / 0.34 ( 5363) covalent geometry : angle 1.02618 / 0.51 ( 7576) hydrogen bonds : bond 0.06853 / 4.99 ( 298) hydrogen bonds : angle 8.29986 / 5.78 ( 794) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1049.92 seconds wall clock time: 18 minutes 38.33 seconds (1118.33 seconds total)