Starting phenix.real_space_refine on Fri Aug 22 19:45:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b0m_15788/08_2025/8b0m_15788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0m_15788/08_2025/8b0m_15788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.01 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b0m_15788/08_2025/8b0m_15788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0m_15788/08_2025/8b0m_15788.map" model { file = "/net/cci-nas-00/data/ceres_data/8b0m_15788/08_2025/8b0m_15788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0m_15788/08_2025/8b0m_15788.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.034 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3853 atoms to isotropic. 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 1 5.49 5 S 14 5.16 5 C 2648 2.51 5 N 656 2.21 5 O 696 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s 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: 4015 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3965 Classifications: {'peptide': 508} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 36, 'TRANS': 471} Unresolved non-hydrogen bonds: 33 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1, 'ASP:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.15, per 1000 atoms: 0.29 Number of scatterers: 4015 At special positions: 0 Unit cell: (59.472, 83.426, 84.252, 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) S 14 16.00 P 1 15.00 O 696 8.00 N 656 7.00 C 2648 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: 0.31 Conformation dependent library (CDL) restraints added in 113.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 936 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 4 sheets defined 59.4% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 9 through 23 Processing helix chain 'A' and resid 24 through 28 removed outlier: 3.599A pdb=" N PHE A 28 " --> pdb=" O THR A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 47 removed outlier: 3.919A pdb=" N ILE A 38 " --> pdb=" O TRP A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 69 removed outlier: 3.509A pdb=" N ALA A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 81 removed outlier: 3.527A pdb=" N SER A 78 " --> pdb=" O TRP A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 116 removed outlier: 4.200A pdb=" N TYR A 104 " --> pdb=" O TYR A 100 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR A 105 " --> pdb=" O LEU A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 126 Processing helix chain 'A' and resid 127 through 140 Processing helix chain 'A' and resid 141 through 145 removed outlier: 3.839A pdb=" N THR A 144 " --> pdb=" O TRP A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 155 removed outlier: 4.022A pdb=" N SER A 154 " --> pdb=" O GLN A 150 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 150 through 155' Processing helix chain 'A' and resid 156 through 157 No H-bonds generated for 'chain 'A' and resid 156 through 157' Processing helix chain 'A' and resid 158 through 162 removed outlier: 4.607A pdb=" N GLY A 162 " --> pdb=" O PRO A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 168 Processing helix chain 'A' and resid 168 through 189 removed outlier: 3.894A pdb=" N ILE A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 204 removed outlier: 3.965A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 211 Processing helix chain 'A' and resid 238 through 240 No H-bonds generated for 'chain 'A' and resid 238 through 240' Processing helix chain 'A' and resid 241 through 257 Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 277 through 292 removed outlier: 3.611A pdb=" N LEU A 281 " --> pdb=" O GLN A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 349 removed outlier: 4.441A pdb=" N SER A 349 " --> pdb=" O PRO A 346 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.694A pdb=" N LEU A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA A 355 " --> pdb=" O LEU A 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 350 through 355' Processing helix chain 'A' and resid 356 through 359 Processing helix chain 'A' and resid 386 through 391 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 412 through 417 removed outlier: 4.385A pdb=" N TRP A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N GLY A 417 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 437 removed outlier: 3.570A pdb=" N ARG A 432 " --> pdb=" O MET A 428 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ALA A 433 " --> pdb=" O ALA A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 487 Processing helix chain 'A' and resid 488 through 508 removed outlier: 4.087A pdb=" N MET A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 215 through 216 Processing sheet with id=AA2, first strand: chain 'A' and resid 270 through 273 removed outlier: 3.940A pdb=" N VAL A 300 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP A 272 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 270 through 273 removed outlier: 3.940A pdb=" N VAL A 300 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASP A 272 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N ILE A 263 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 8.138A pdb=" N GLY A 298 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N LEU A 262 " --> pdb=" O GLN A 223 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 375 through 377 removed outlier: 6.534A pdb=" N GLU A 381 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU A 408 " --> pdb=" O GLU A 381 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N THR A 383 " --> pdb=" O LEU A 408 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE A 410 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N LEU A 407 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 7.673A pdb=" N SER A 443 " --> pdb=" O LEU A 407 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N THR A 409 " --> pdb=" O SER A 443 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N VAL A 451 " --> pdb=" O GLN A 459 " (cutoff:3.500A) 204 hydrogen bonds defined for protein. 543 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: 0.60 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 613 1.31 - 1.43: 1113 1.43 - 1.56: 2374 1.56 - 1.68: 2 1.68 - 1.80: 26 Bond restraints: 4128 Sorted by residual: bond pdb=" C8 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 1.331 1.399 -0.068 2.00e-02 2.50e+03 1.15e+01 bond pdb=" C30 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 1.331 1.398 -0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C6 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 1.432 1.396 0.036 2.00e-02 2.50e+03 3.18e+00 bond pdb=" C1 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 1.427 1.396 0.031 2.00e-02 2.50e+03 2.36e+00 bond pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " ideal model delta sigma weight residual 1.420 1.398 0.022 2.00e-02 2.50e+03 1.23e+00 ... (remaining 4123 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 5579 3.27 - 6.55: 49 6.55 - 9.82: 2 9.82 - 13.09: 1 13.09 - 16.37: 1 Bond angle restraints: 5632 Sorted by residual: angle pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O14 PTY A 601 " ideal model delta sigma weight residual 92.90 109.27 -16.37 3.00e+00 1.11e-01 2.98e+01 angle pdb=" O12 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O13 PTY A 601 " ideal model delta sigma weight residual 119.61 109.68 9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" C11 PTY A 601 " pdb=" C8 PTY A 601 " pdb=" O7 PTY A 601 " ideal model delta sigma weight residual 111.29 119.69 -8.40 3.00e+00 1.11e-01 7.83e+00 angle pdb=" C31 PTY A 601 " pdb=" C30 PTY A 601 " pdb=" O4 PTY A 601 " ideal model delta sigma weight residual 111.62 119.81 -8.19 3.00e+00 1.11e-01 7.46e+00 angle pdb=" N GLU A 219 " pdb=" CA GLU A 219 " pdb=" C GLU A 219 " ideal model delta sigma weight residual 113.18 109.62 3.56 1.33e+00 5.65e-01 7.15e+00 ... (remaining 5627 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.60: 2347 22.60 - 45.21: 66 45.21 - 67.81: 11 67.81 - 90.41: 1 90.41 - 113.02: 1 Dihedral angle restraints: 2426 sinusoidal: 966 harmonic: 1460 Sorted by residual: dihedral pdb=" CA GLY A 71 " pdb=" C GLY A 71 " pdb=" N ILE A 72 " pdb=" CA ILE A 72 " ideal model delta harmonic sigma weight residual 180.00 155.62 24.38 0 5.00e+00 4.00e-02 2.38e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual -59.77 53.25 -113.02 1 3.00e+01 1.11e-03 1.48e+01 dihedral pdb=" CA PHE A 28 " pdb=" C PHE A 28 " pdb=" N SER A 29 " pdb=" CA SER A 29 " ideal model delta harmonic sigma weight residual -180.00 -161.99 -18.01 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 2423 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 374 0.029 - 0.057: 165 0.057 - 0.086: 49 0.086 - 0.114: 38 0.114 - 0.143: 8 Chirality restraints: 634 Sorted by residual: chirality pdb=" CA TRP A 489 " pdb=" N TRP A 489 " pdb=" C TRP A 489 " pdb=" CB TRP A 489 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA ILE A 316 " pdb=" N ILE A 316 " pdb=" C ILE A 316 " pdb=" CB ILE A 316 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 chirality pdb=" CA ILE A 72 " pdb=" N ILE A 72 " pdb=" C ILE A 72 " pdb=" CB ILE A 72 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.02e-01 ... (remaining 631 not shown) Planarity restraints: 705 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 421 " -0.027 5.00e-02 4.00e+02 4.12e-02 2.72e+00 pdb=" N PRO A 422 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 422 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 422 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 87 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.53e+00 pdb=" N PRO A 88 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 88 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 88 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 204 " -0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 205 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 205 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 205 " -0.019 5.00e-02 4.00e+02 ... (remaining 702 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 939 2.79 - 3.31: 3875 3.31 - 3.84: 6778 3.84 - 4.37: 8433 4.37 - 4.90: 14419 Nonbonded interactions: 34444 Sorted by model distance: nonbonded pdb=" O VAL A 77 " pdb=" OG1 THR A 81 " model vdw 2.258 3.040 nonbonded pdb=" OH TYR A 333 " pdb=" OE1 GLU A 389 " model vdw 2.269 3.040 nonbonded pdb=" OE1 GLU A 274 " pdb=" NH2 ARG A 332 " model vdw 2.303 3.120 nonbonded pdb=" O ALA A 98 " pdb=" OG SER A 102 " model vdw 2.327 3.040 nonbonded pdb=" OE1 GLU A 136 " pdb=" NH2 ARG A 139 " model vdw 2.344 3.120 ... (remaining 34439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.730 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 4128 Z= 0.153 Angle : 0.656 16.367 5632 Z= 0.283 Chirality : 0.042 0.143 634 Planarity : 0.005 0.041 705 Dihedral : 11.178 113.017 1490 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.48 % Allowed : 2.40 % Favored : 97.12 % 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: -0.18 (0.39), residues: 506 helix: 0.33 (0.34), residues: 229 sheet: 0.42 (0.73), residues: 65 loop : -0.68 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 52 TYR 0.008 0.001 TYR A 31 PHE 0.009 0.001 PHE A 28 TRP 0.006 0.001 TRP A 34 HIS 0.001 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4128) covalent geometry : angle 0.65568 ( 5632) hydrogen bonds : bond 0.25505 ( 203) hydrogen bonds : angle 8.63661 ( 543) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.153 Fit side-chains REVERT: A 11 ARG cc_start: 0.7011 (mtt90) cc_final: 0.6811 (mtm180) REVERT: A 238 ASP cc_start: 0.8267 (m-30) cc_final: 0.7863 (m-30) REVERT: A 247 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8431 (ttmm) REVERT: A 278 GLN cc_start: 0.9247 (tp-100) cc_final: 0.9037 (tp40) REVERT: A 282 LYS cc_start: 0.8595 (mttt) cc_final: 0.8270 (mttp) outliers start: 2 outliers final: 2 residues processed: 73 average time/residue: 0.0777 time to fit residues: 6.9952 Evaluate side-chains 44 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.123276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.091098 restraints weight = 5166.628| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 2.43 r_work: 0.2851 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4128 Z= 0.151 Angle : 0.567 5.899 5632 Z= 0.289 Chirality : 0.045 0.170 634 Planarity : 0.005 0.042 705 Dihedral : 9.633 77.337 594 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.72 % Allowed : 7.21 % Favored : 92.07 % 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: 0.08 (0.39), residues: 506 helix: 0.76 (0.34), residues: 231 sheet: 0.21 (0.75), residues: 60 loop : -0.69 (0.46), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 123 TYR 0.008 0.001 TYR A 31 PHE 0.016 0.001 PHE A 500 TRP 0.009 0.001 TRP A 34 HIS 0.002 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 4128) covalent geometry : angle 0.56712 ( 5632) hydrogen bonds : bond 0.04387 ( 203) hydrogen bonds : angle 5.41074 ( 543) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.116 Fit side-chains REVERT: A 11 ARG cc_start: 0.6982 (mtt90) cc_final: 0.6468 (mtm180) REVERT: A 19 LEU cc_start: 0.6940 (mt) cc_final: 0.6593 (tp) REVERT: A 238 ASP cc_start: 0.8378 (m-30) cc_final: 0.7916 (m-30) REVERT: A 247 LYS cc_start: 0.8574 (ttpp) cc_final: 0.8309 (ttmm) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.0619 time to fit residues: 3.8501 Evaluate side-chains 39 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.0020 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.123189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.091058 restraints weight = 5098.955| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.43 r_work: 0.2859 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4128 Z= 0.128 Angle : 0.537 5.802 5632 Z= 0.270 Chirality : 0.044 0.162 634 Planarity : 0.005 0.043 705 Dihedral : 9.182 63.772 594 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.16 % Allowed : 6.73 % Favored : 91.11 % 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: 0.17 (0.39), residues: 506 helix: 0.98 (0.34), residues: 232 sheet: 0.24 (0.72), residues: 62 loop : -0.86 (0.47), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 123 TYR 0.008 0.001 TYR A 104 PHE 0.012 0.001 PHE A 174 TRP 0.008 0.001 TRP A 34 HIS 0.001 0.001 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4128) covalent geometry : angle 0.53734 ( 5632) hydrogen bonds : bond 0.03783 ( 203) hydrogen bonds : angle 4.98418 ( 543) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.150 Fit side-chains REVERT: A 19 LEU cc_start: 0.6824 (mt) cc_final: 0.6552 (tp) REVERT: A 238 ASP cc_start: 0.8425 (m-30) cc_final: 0.7920 (m-30) REVERT: A 247 LYS cc_start: 0.8558 (ttpp) cc_final: 0.8286 (ttmm) outliers start: 9 outliers final: 9 residues processed: 47 average time/residue: 0.0521 time to fit residues: 3.3213 Evaluate side-chains 48 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 12 optimal weight: 0.0010 chunk 41 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.124346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.092473 restraints weight = 5062.069| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.43 r_work: 0.2883 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4128 Z= 0.114 Angle : 0.520 5.761 5632 Z= 0.260 Chirality : 0.043 0.158 634 Planarity : 0.005 0.043 705 Dihedral : 8.748 67.534 594 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.40 % Allowed : 7.21 % Favored : 90.38 % 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: 0.29 (0.40), residues: 506 helix: 1.22 (0.35), residues: 233 sheet: -0.26 (0.64), residues: 76 loop : -0.80 (0.49), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.008 0.001 TYR A 104 PHE 0.012 0.001 PHE A 500 TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 425 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 4128) covalent geometry : angle 0.51988 ( 5632) hydrogen bonds : bond 0.03292 ( 203) hydrogen bonds : angle 4.72522 ( 543) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.104 Fit side-chains REVERT: A 238 ASP cc_start: 0.8426 (m-30) cc_final: 0.7945 (m-30) REVERT: A 247 LYS cc_start: 0.8539 (ttpp) cc_final: 0.8254 (ttmm) outliers start: 10 outliers final: 9 residues processed: 53 average time/residue: 0.0496 time to fit residues: 3.5471 Evaluate side-chains 52 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 21 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 23 optimal weight: 0.0870 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 overall best weight: 0.7762 ------------------------------------------------------------------------------- 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 = 0.3430 r_free = 0.3430 target = 0.124055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.093422 restraints weight = 4987.379| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.32 r_work: 0.2909 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4128 Z= 0.133 Angle : 0.537 5.799 5632 Z= 0.267 Chirality : 0.044 0.160 634 Planarity : 0.005 0.044 705 Dihedral : 8.413 73.722 594 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.88 % Allowed : 7.45 % Favored : 89.66 % 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: 0.35 (0.40), residues: 506 helix: 1.37 (0.35), residues: 233 sheet: -0.34 (0.64), residues: 76 loop : -0.86 (0.49), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 367 TYR 0.010 0.001 TYR A 104 PHE 0.012 0.001 PHE A 174 TRP 0.007 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 4128) covalent geometry : angle 0.53665 ( 5632) hydrogen bonds : bond 0.03354 ( 203) hydrogen bonds : angle 4.71067 ( 543) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.110 Fit side-chains REVERT: A 19 LEU cc_start: 0.7248 (OUTLIER) cc_final: 0.6710 (tp) REVERT: A 238 ASP cc_start: 0.8478 (m-30) cc_final: 0.7999 (m-30) REVERT: A 239 GLU cc_start: 0.8604 (mm-30) cc_final: 0.8402 (mm-30) REVERT: A 247 LYS cc_start: 0.8639 (ttpp) cc_final: 0.8347 (ttmm) outliers start: 12 outliers final: 11 residues processed: 49 average time/residue: 0.0489 time to fit residues: 3.3085 Evaluate side-chains 54 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 9 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 3 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3428 r_free = 0.3428 target = 0.123981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.093188 restraints weight = 5088.608| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.34 r_work: 0.2906 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4128 Z= 0.132 Angle : 0.529 5.778 5632 Z= 0.264 Chirality : 0.044 0.158 634 Planarity : 0.005 0.045 705 Dihedral : 8.233 80.869 594 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.12 % Allowed : 7.45 % Favored : 89.42 % 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: 0.45 (0.40), residues: 506 helix: 1.50 (0.35), residues: 233 sheet: -0.26 (0.65), residues: 76 loop : -0.89 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.009 0.001 TYR A 104 PHE 0.011 0.001 PHE A 500 TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 4128) covalent geometry : angle 0.52912 ( 5632) hydrogen bonds : bond 0.03259 ( 203) hydrogen bonds : angle 4.60945 ( 543) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.098 Fit side-chains REVERT: A 19 LEU cc_start: 0.7249 (OUTLIER) cc_final: 0.6710 (tp) REVERT: A 238 ASP cc_start: 0.8491 (m-30) cc_final: 0.7996 (m-30) REVERT: A 239 GLU cc_start: 0.8571 (mm-30) cc_final: 0.8352 (mm-30) REVERT: A 247 LYS cc_start: 0.8670 (ttpp) cc_final: 0.8375 (ttmm) outliers start: 13 outliers final: 12 residues processed: 51 average time/residue: 0.0441 time to fit residues: 3.1361 Evaluate side-chains 57 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 12 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.125072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094284 restraints weight = 5013.019| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 2.33 r_work: 0.2920 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4128 Z= 0.116 Angle : 0.525 6.144 5632 Z= 0.262 Chirality : 0.043 0.167 634 Planarity : 0.005 0.045 705 Dihedral : 8.137 86.039 594 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.12 % Allowed : 8.17 % Favored : 88.70 % 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: 0.53 (0.40), residues: 506 helix: 1.59 (0.35), residues: 233 sheet: -0.17 (0.65), residues: 76 loop : -0.91 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 52 TYR 0.009 0.001 TYR A 104 PHE 0.011 0.001 PHE A 500 TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4128) covalent geometry : angle 0.52486 ( 5632) hydrogen bonds : bond 0.03171 ( 203) hydrogen bonds : angle 4.55164 ( 543) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.095 Fit side-chains REVERT: A 19 LEU cc_start: 0.7229 (OUTLIER) cc_final: 0.6685 (tp) REVERT: A 238 ASP cc_start: 0.8534 (m-30) cc_final: 0.8032 (m-30) REVERT: A 239 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8319 (mm-30) REVERT: A 247 LYS cc_start: 0.8641 (ttpp) cc_final: 0.8346 (ttmm) outliers start: 13 outliers final: 12 residues processed: 54 average time/residue: 0.0454 time to fit residues: 3.3659 Evaluate side-chains 60 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.125737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.093832 restraints weight = 5004.890| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.41 r_work: 0.2916 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.2005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4128 Z= 0.133 Angle : 0.535 5.776 5632 Z= 0.268 Chirality : 0.044 0.158 634 Planarity : 0.005 0.044 705 Dihedral : 8.121 89.447 594 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.12 % Allowed : 7.69 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.40), residues: 506 helix: 1.60 (0.35), residues: 233 sheet: -0.15 (0.65), residues: 76 loop : -0.93 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 139 TYR 0.009 0.001 TYR A 104 PHE 0.012 0.001 PHE A 174 TRP 0.007 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 4128) covalent geometry : angle 0.53488 ( 5632) hydrogen bonds : bond 0.03256 ( 203) hydrogen bonds : angle 4.59597 ( 543) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.108 Fit side-chains REVERT: A 19 LEU cc_start: 0.7308 (OUTLIER) cc_final: 0.6763 (tp) REVERT: A 85 MET cc_start: 0.8222 (mtm) cc_final: 0.7635 (ptp) REVERT: A 235 LEU cc_start: 0.8643 (tp) cc_final: 0.8426 (tp) REVERT: A 238 ASP cc_start: 0.8543 (m-30) cc_final: 0.8074 (m-30) REVERT: A 239 GLU cc_start: 0.8533 (mm-30) cc_final: 0.8291 (mm-30) REVERT: A 247 LYS cc_start: 0.8697 (ttpp) cc_final: 0.8398 (ttmm) outliers start: 13 outliers final: 12 residues processed: 52 average time/residue: 0.0408 time to fit residues: 2.8819 Evaluate side-chains 59 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 28 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3445 r_free = 0.3445 target = 0.125140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094294 restraints weight = 5057.864| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.35 r_work: 0.2920 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4128 Z= 0.128 Angle : 0.533 5.912 5632 Z= 0.266 Chirality : 0.044 0.163 634 Planarity : 0.005 0.045 705 Dihedral : 7.936 85.783 594 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.12 % Allowed : 7.93 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.58 (0.40), residues: 506 helix: 1.65 (0.35), residues: 233 sheet: -0.10 (0.65), residues: 76 loop : -0.94 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 52 TYR 0.009 0.001 TYR A 104 PHE 0.012 0.001 PHE A 500 TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4128) covalent geometry : angle 0.53284 ( 5632) hydrogen bonds : bond 0.03212 ( 203) hydrogen bonds : angle 4.57810 ( 543) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.152 Fit side-chains REVERT: A 19 LEU cc_start: 0.7335 (OUTLIER) cc_final: 0.6801 (tp) REVERT: A 85 MET cc_start: 0.8237 (mtm) cc_final: 0.7620 (ptp) REVERT: A 238 ASP cc_start: 0.8551 (m-30) cc_final: 0.8053 (m-30) REVERT: A 239 GLU cc_start: 0.8520 (mm-30) cc_final: 0.8277 (mm-30) REVERT: A 247 LYS cc_start: 0.8711 (ttpp) cc_final: 0.8409 (ttmm) outliers start: 13 outliers final: 12 residues processed: 53 average time/residue: 0.0500 time to fit residues: 3.6625 Evaluate side-chains 59 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.0570 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 0 optimal weight: 0.7980 chunk 30 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3459 r_free = 0.3459 target = 0.126347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.095574 restraints weight = 4929.610| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.32 r_work: 0.2935 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4128 Z= 0.115 Angle : 0.525 5.746 5632 Z= 0.262 Chirality : 0.043 0.157 634 Planarity : 0.005 0.045 705 Dihedral : 7.732 80.779 594 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 3.12 % Allowed : 7.93 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.68 (0.40), residues: 506 helix: 1.75 (0.35), residues: 233 sheet: -0.05 (0.65), residues: 76 loop : -0.92 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 397 TYR 0.009 0.001 TYR A 104 PHE 0.011 0.001 PHE A 500 TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 4128) covalent geometry : angle 0.52538 ( 5632) hydrogen bonds : bond 0.03162 ( 203) hydrogen bonds : angle 4.56416 ( 543) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.094 Fit side-chains REVERT: A 19 LEU cc_start: 0.7208 (OUTLIER) cc_final: 0.6690 (tp) REVERT: A 85 MET cc_start: 0.8177 (mtm) cc_final: 0.7731 (ptp) REVERT: A 238 ASP cc_start: 0.8527 (m-30) cc_final: 0.8016 (m-30) REVERT: A 239 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8264 (mm-30) REVERT: A 247 LYS cc_start: 0.8675 (ttpp) cc_final: 0.8374 (ttmm) outliers start: 13 outliers final: 12 residues processed: 52 average time/residue: 0.0496 time to fit residues: 3.5333 Evaluate side-chains 58 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 42 MET Chi-restraints excluded: chain A residue 144 THR Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 45 optimal weight: 0.0370 chunk 39 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 33 optimal weight: 0.0470 chunk 17 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4956 ------------------------------------------------------------------------------- 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 = 0.3465 r_free = 0.3465 target = 0.126735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.096422 restraints weight = 4974.062| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.29 r_work: 0.2950 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 4128 Z= 0.110 Angle : 0.526 6.004 5632 Z= 0.262 Chirality : 0.043 0.164 634 Planarity : 0.005 0.045 705 Dihedral : 7.566 77.603 594 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.88 % Allowed : 8.17 % Favored : 88.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.72 (0.40), residues: 506 helix: 1.80 (0.35), residues: 233 sheet: -0.03 (0.65), residues: 76 loop : -0.92 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 139 TYR 0.008 0.001 TYR A 104 PHE 0.011 0.001 PHE A 500 TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 4128) covalent geometry : angle 0.52594 ( 5632) hydrogen bonds : bond 0.03071 ( 203) hydrogen bonds : angle 4.54941 ( 543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1060.56 seconds wall clock time: 18 minutes 45.59 seconds (1125.59 seconds total)