Starting phenix.real_space_refine on Thu Jul 2 06:54:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b0m_15788/07_2026/8b0m_15788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0m_15788/07_2026/8b0m_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 { model { file = "/net/cci-nas-00/data/ceres_data/8b0m_15788/07_2026/8b0m_15788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0m_15788/07_2026/8b0m_15788.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8b0m_15788/07_2026/8b0m_15788.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b0m_15788/07_2026/8b0m_15788.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b0m_15788/07_2026/8b0m_15788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0m_15788/07_2026/8b0m_15788.map" } 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-dev-6108/lib/python3.11/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: 1.04, per 1000 atoms: 0.26 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: 0.37 Conformation dependent library (CDL) restraints added in 155.0 milliseconds 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: 0.14 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: 0.72 Time building geometry restraints manager: 0.51 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: 62 45.21 - 67.81: 9 67.81 - 90.41: 1 90.41 - 113.02: 1 Dihedral angle restraints: 2420 sinusoidal: 960 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 2417 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: 1.070 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 6.140 Find NCS groups from input model: 0.020 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:1.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 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 : 10.773 113.017 1484 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 are 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/Z covalent geometry : bond 0.00345 / 0.15 ( 4128) covalent geometry : angle 0.65568 / 0.28 ( 5632) hydrogen bonds : bond 0.25505 / 16.93 ( 203) hydrogen bonds : angle 8.63661 / 6.29 ( 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 : 0.148 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: 0.0853 time to fit residues: 7.6505 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 : 0.159 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.122614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.090499 restraints weight = 5183.423| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 2.43 r_work: 0.2842 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4128 Z= 0.158 Angle : 0.573 5.934 5632 Z= 0.292 Chirality : 0.045 0.171 634 Planarity : 0.005 0.042 705 Dihedral : 8.698 80.579 588 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.72 % Allowed : 6.97 % Favored : 92.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.39), residues: 506 helix: 0.76 (0.34), residues: 231 sheet: 0.21 (0.71), residues: 63 loop : -0.70 (0.47), residues: 212 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 0.017 0.001 PHE A 500 TRP 0.010 0.001 TRP A 34 HIS 0.002 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00364 / 0.16 ( 4128) covalent geometry : angle 0.57306 / 0.29 ( 5632) hydrogen bonds : bond 0.04677 / 3.06 ( 203) hydrogen bonds : angle 5.46909 / 4.04 ( 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 : 0.150 Fit side-chains REVERT: A 11 ARG cc_start: 0.6964 (mtt90) cc_final: 0.6326 (mtm180) REVERT: A 19 LEU cc_start: 0.6939 (mt) cc_final: 0.6605 (tp) REVERT: A 238 ASP cc_start: 0.8381 (m-30) cc_final: 0.7917 (m-30) REVERT: A 247 LYS cc_start: 0.8572 (ttpp) cc_final: 0.8307 (ttmm) outliers start: 3 outliers final: 3 residues processed: 49 average time/residue: 0.0795 time to fit residues: 4.9663 Evaluate side-chains 38 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.124 ------------------------------------------------------------------------------- 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: 2.9990 chunk 8 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.0570 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.123404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.091506 restraints weight = 5094.400| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.43 r_work: 0.2866 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4128 Z= 0.125 Angle : 0.535 5.795 5632 Z= 0.269 Chirality : 0.044 0.161 634 Planarity : 0.005 0.042 705 Dihedral : 8.248 67.688 588 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.40 % Allowed : 6.49 % 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 are not related in a simple way. whole: 0.19 (0.39), residues: 506 helix: 1.02 (0.34), residues: 232 sheet: 0.24 (0.72), residues: 62 loop : -0.87 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 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/Z covalent geometry : bond 0.00282 / 0.12 ( 4128) covalent geometry : angle 0.53466 / 0.27 ( 5632) hydrogen bonds : bond 0.03732 / 2.43 ( 203) hydrogen bonds : angle 4.94236 / 3.71 ( 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 51 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 41 time to evaluate : 0.091 Fit side-chains REVERT: A 19 LEU cc_start: 0.6811 (mt) cc_final: 0.6547 (tp) REVERT: A 238 ASP cc_start: 0.8432 (m-30) cc_final: 0.7923 (m-30) REVERT: A 247 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8285 (ttmm) outliers start: 10 outliers final: 9 residues processed: 47 average time/residue: 0.0546 time to fit residues: 3.4521 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 : 0.091 ------------------------------------------------------------------------------- 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=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: 0.0980 chunk 44 optimal weight: 0.0670 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 12 optimal weight: 0.0040 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 13 optimal weight: 0.7980 overall best weight: 0.3530 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.126198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.095056 restraints weight = 5042.163| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 2.38 r_work: 0.2914 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2772 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4128 Z= 0.102 Angle : 0.509 5.738 5632 Z= 0.254 Chirality : 0.043 0.156 634 Planarity : 0.005 0.043 705 Dihedral : 7.680 59.654 588 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.16 % Allowed : 7.45 % 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 are not related in a simple way. whole: 0.39 (0.40), residues: 506 helix: 1.33 (0.35), residues: 233 sheet: -0.22 (0.64), residues: 76 loop : -0.79 (0.49), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 430 TYR 0.006 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/Z covalent geometry : bond 0.00223 / 0.10 ( 4128) covalent geometry : angle 0.50884 / 0.25 ( 5632) hydrogen bonds : bond 0.03132 / 2.04 ( 203) hydrogen bonds : angle 4.66399 / 3.52 ( 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: 9 poor density : 47 time to evaluate : 0.143 Fit side-chains REVERT: A 19 LEU cc_start: 0.6801 (mt) cc_final: 0.6542 (tp) REVERT: A 238 ASP cc_start: 0.8478 (m-30) cc_final: 0.7971 (m-30) REVERT: A 247 LYS cc_start: 0.8576 (ttpp) cc_final: 0.8297 (ttmm) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.0530 time to fit residues: 3.8142 Evaluate side-chains 50 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.148 ------------------------------------------------------------------------------- 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 260 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 315 THR 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: 4.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.119479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.087553 restraints weight = 5079.486| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.38 r_work: 0.2836 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2690 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.2690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.1776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 4128 Z= 0.282 Angle : 0.636 6.083 5632 Z= 0.320 Chirality : 0.048 0.181 634 Planarity : 0.005 0.045 705 Dihedral : 7.828 57.657 588 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.88 % Allowed : 6.97 % Favored : 90.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.39), residues: 506 helix: 1.03 (0.34), residues: 233 sheet: -0.23 (0.69), residues: 68 loop : -0.94 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 13 TYR 0.015 0.002 TYR A 104 PHE 0.018 0.002 PHE A 174 TRP 0.007 0.001 TRP A 63 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00688 / 0.28 ( 4128) covalent geometry : angle 0.63570 / 0.32 ( 5632) hydrogen bonds : bond 0.04199 / 2.74 ( 203) hydrogen bonds : angle 4.95050 / 3.70 ( 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 50 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.157 Fit side-chains REVERT: A 238 ASP cc_start: 0.8501 (m-30) cc_final: 0.8062 (m-30) REVERT: A 247 LYS cc_start: 0.8703 (ttpp) cc_final: 0.8413 (ttmm) outliers start: 12 outliers final: 10 residues processed: 47 average time/residue: 0.0546 time to fit residues: 3.5642 Evaluate side-chains 48 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 33 VAL Chi-restraints excluded: chain A residue 91 ILE 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 315 THR 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: 1.9990 chunk 40 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.122595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.090570 restraints weight = 5136.314| |-----------------------------------------------------------------------------| r_work (start): 0.3004 rms_B_bonded: 2.42 r_work: 0.2868 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4128 Z= 0.148 Angle : 0.549 5.820 5632 Z= 0.276 Chirality : 0.044 0.159 634 Planarity : 0.005 0.044 705 Dihedral : 7.529 56.917 588 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.88 % Allowed : 7.69 % 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 are not related in a simple way. whole: 0.19 (0.39), residues: 506 helix: 1.25 (0.35), residues: 233 sheet: -0.45 (0.64), 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 0.010 0.001 TYR A 104 PHE 0.013 0.001 PHE A 174 TRP 0.010 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 ( 4128) covalent geometry : angle 0.54927 / 0.28 ( 5632) hydrogen bonds : bond 0.03496 / 2.29 ( 203) hydrogen bonds : angle 4.73574 / 3.56 ( 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 54 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.162 Fit side-chains REVERT: A 79 ILE cc_start: 0.8749 (mt) cc_final: 0.8484 (mp) REVERT: A 238 ASP cc_start: 0.8468 (m-30) cc_final: 0.7977 (m-30) REVERT: A 247 LYS cc_start: 0.8620 (ttpp) cc_final: 0.8336 (ttmm) outliers start: 12 outliers final: 12 residues processed: 50 average time/residue: 0.0541 time to fit residues: 3.7607 Evaluate side-chains 52 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.147 ------------------------------------------------------------------------------- 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 91 ILE 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 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: 0.9980 chunk 13 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.122484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.091629 restraints weight = 5061.822| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.32 r_work: 0.2891 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2748 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4128 Z= 0.142 Angle : 0.553 6.787 5632 Z= 0.275 Chirality : 0.044 0.173 634 Planarity : 0.005 0.045 705 Dihedral : 7.341 56.441 588 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.66 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 are not related in a simple way. whole: 0.32 (0.40), residues: 506 helix: 1.39 (0.35), residues: 233 sheet: -0.38 (0.63), residues: 76 loop : -0.93 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 13 TYR 0.010 0.001 TYR A 104 PHE 0.012 0.001 PHE A 174 TRP 0.009 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.14 ( 4128) covalent geometry : angle 0.55312 / 0.27 ( 5632) hydrogen bonds : bond 0.03364 / 2.21 ( 203) hydrogen bonds : angle 4.61278 / 3.49 ( 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 55 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.149 Fit side-chains REVERT: A 19 LEU cc_start: 0.7268 (OUTLIER) cc_final: 0.6728 (tp) REVERT: A 79 ILE cc_start: 0.8759 (mt) cc_final: 0.8508 (mp) REVERT: A 238 ASP cc_start: 0.8497 (m-30) cc_final: 0.8031 (m-30) REVERT: A 247 LYS cc_start: 0.8687 (ttpp) cc_final: 0.8394 (ttmm) outliers start: 13 outliers final: 12 residues processed: 49 average time/residue: 0.0522 time to fit residues: 3.5608 Evaluate side-chains 56 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 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 91 ILE 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 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: 0.8980 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 8 optimal weight: 0.1980 chunk 27 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 43 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.123064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.092631 restraints weight = 4986.253| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 2.32 r_work: 0.2913 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2004 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= 0.122 Angle : 0.532 5.757 5632 Z= 0.265 Chirality : 0.043 0.158 634 Planarity : 0.005 0.045 705 Dihedral : 7.161 56.051 588 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.12 % Allowed : 8.41 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.40), residues: 506 helix: 1.53 (0.35), residues: 233 sheet: -0.30 (0.64), residues: 76 loop : -0.92 (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 0.010 0.001 TRP A 34 HIS 0.001 0.000 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 4128) covalent geometry : angle 0.53232 / 0.26 ( 5632) hydrogen bonds : bond 0.03166 / 2.08 ( 203) hydrogen bonds : angle 4.51609 / 3.43 ( 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 60 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.154 Fit side-chains REVERT: A 19 LEU cc_start: 0.7228 (OUTLIER) cc_final: 0.6711 (tp) REVERT: A 79 ILE cc_start: 0.8794 (mt) cc_final: 0.8404 (mp) REVERT: A 238 ASP cc_start: 0.8504 (m-30) cc_final: 0.8054 (m-30) REVERT: A 247 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8369 (ttmm) outliers start: 13 outliers final: 11 residues processed: 53 average time/residue: 0.0595 time to fit residues: 4.2255 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 : 0.155 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.0870 chunk 38 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 241 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.093592 restraints weight = 5092.116| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 2.33 r_work: 0.2922 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2058 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= 0.117 Angle : 0.530 5.853 5632 Z= 0.262 Chirality : 0.044 0.166 634 Planarity : 0.005 0.045 705 Dihedral : 7.048 57.264 588 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % 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 are not related in a simple way. whole: 0.56 (0.40), residues: 506 helix: 1.64 (0.35), residues: 233 sheet: -0.27 (0.64), residues: 76 loop : -0.88 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 485 TYR 0.009 0.001 TYR A 104 PHE 0.011 0.001 PHE A 500 TRP 0.009 0.001 TRP A 34 HIS 0.001 0.001 HIS A 425 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 4128) covalent geometry : angle 0.52989 / 0.26 ( 5632) hydrogen bonds : bond 0.03128 / 2.05 ( 203) hydrogen bonds : angle 4.46772 / 3.40 ( 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 59 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.143 Fit side-chains REVERT: A 19 LEU cc_start: 0.7168 (OUTLIER) cc_final: 0.6695 (tp) REVERT: A 79 ILE cc_start: 0.8792 (mt) cc_final: 0.8416 (mp) REVERT: A 238 ASP cc_start: 0.8512 (m-30) cc_final: 0.8084 (m-30) REVERT: A 247 LYS cc_start: 0.8656 (ttpp) cc_final: 0.8354 (ttmm) outliers start: 13 outliers final: 12 residues processed: 52 average time/residue: 0.0518 time to fit residues: 3.7460 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 : 0.146 ------------------------------------------------------------------------------- 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: 1.9990 chunk 45 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 33 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.125061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.094591 restraints weight = 4958.814| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.31 r_work: 0.2930 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2786 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4128 Z= 0.110 Angle : 0.525 5.736 5632 Z= 0.260 Chirality : 0.043 0.157 634 Planarity : 0.005 0.045 705 Dihedral : 6.959 58.318 588 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.37 % Allowed : 7.69 % 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 are not related in a simple way. whole: 0.62 (0.40), residues: 506 helix: 1.71 (0.35), residues: 233 sheet: -0.22 (0.65), residues: 76 loop : -0.89 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 485 TYR 0.008 0.001 TYR A 104 PHE 0.011 0.001 PHE A 500 TRP 0.009 0.001 TRP A 34 HIS 0.001 0.001 HIS A 337 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 ( 4128) covalent geometry : angle 0.52464 / 0.26 ( 5632) hydrogen bonds : bond 0.03022 / 1.99 ( 203) hydrogen bonds : angle 4.44566 / 3.39 ( 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: 14 poor density : 45 time to evaluate : 0.155 Fit side-chains REVERT: A 19 LEU cc_start: 0.7122 (OUTLIER) cc_final: 0.6658 (tp) REVERT: A 238 ASP cc_start: 0.8505 (m-30) cc_final: 0.8034 (m-30) REVERT: A 247 LYS cc_start: 0.8679 (ttpp) cc_final: 0.8367 (ttmm) outliers start: 14 outliers final: 12 residues processed: 52 average time/residue: 0.0529 time to fit residues: 3.8258 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 : 0.150 ------------------------------------------------------------------------------- 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: 1.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3433 r_free = 0.3433 target = 0.124280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.092725 restraints weight = 5051.747| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 2.41 r_work: 0.2898 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4128 Z= 0.129 Angle : 0.540 6.417 5632 Z= 0.267 Chirality : 0.044 0.168 634 Planarity : 0.005 0.045 705 Dihedral : 6.961 58.081 588 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.54 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 are not related in a simple way. whole: 0.61 (0.40), residues: 506 helix: 1.69 (0.35), residues: 233 sheet: -0.21 (0.64), residues: 76 loop : -0.89 (0.49), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 485 TYR 0.010 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/Z covalent geometry : bond 0.00304 / 0.13 ( 4128) covalent geometry : angle 0.54012 / 0.27 ( 5632) hydrogen bonds : bond 0.03155 / 2.07 ( 203) hydrogen bonds : angle 4.46638 / 3.40 ( 543) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1249.25 seconds wall clock time: 22 minutes 5.76 seconds (1325.76 seconds total)