Starting phenix.real_space_refine on Wed Mar 12 06:07:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b0m_15788/03_2025/8b0m_15788.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b0m_15788/03_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_15788/03_2025/8b0m_15788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b0m_15788/03_2025/8b0m_15788.map" model { file = "/net/cci-nas-00/data/ceres_data/8b0m_15788/03_2025/8b0m_15788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b0m_15788/03_2025/8b0m_15788.cif" } resolution = 3.01 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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, 'GLU:plan': 1, 'ARG:plan': 2, 'ASP: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: 3.07, per 1000 atoms: 0.76 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: 0.97 Conformation dependent library (CDL) restraints added in 456.1 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: 0.54 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: 1.27 Time building geometry restraints manager: 1.16 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.480 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:3.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.150 ------------------------------------------------------------------------------- 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= 0.209 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.006 0.001 TRP A 34 HIS 0.001 0.001 HIS A 425 PHE 0.009 0.001 PHE A 28 TYR 0.008 0.001 TYR A 31 ARG 0.001 0.000 ARG A 52 *********************** 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 : 0.413 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: 0.1981 time to fit residues: 17.5949 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 : 0.456 ------------------------------------------------------------------------------- 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 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.0050 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 0.0980 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.124475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.092397 restraints weight = 5072.160| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 2.43 r_work: 0.2870 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.1359 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= 0.179 Angle : 0.556 5.722 5632 Z= 0.283 Chirality : 0.044 0.166 634 Planarity : 0.005 0.042 705 Dihedral : 9.600 78.829 594 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.39), residues: 506 helix: 0.80 (0.34), residues: 231 sheet: 0.26 (0.75), residues: 60 loop : -0.68 (0.47), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 34 HIS 0.001 0.001 HIS A 425 PHE 0.015 0.001 PHE A 500 TYR 0.007 0.001 TYR A 313 ARG 0.002 0.000 ARG A 332 *********************** 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 48 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.470 Fit side-chains REVERT: A 11 ARG cc_start: 0.7007 (mtt90) cc_final: 0.6490 (mtm180) REVERT: A 19 LEU cc_start: 0.6904 (mt) cc_final: 0.6583 (tp) REVERT: A 238 ASP cc_start: 0.8368 (m-30) cc_final: 0.7897 (m-30) REVERT: A 247 LYS cc_start: 0.8568 (ttpp) cc_final: 0.8306 (ttmm) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.1760 time to fit residues: 10.7532 Evaluate side-chains 40 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.437 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 41 optimal weight: 0.0980 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 chunk 6 optimal weight: 1.9990 chunk 37 optimal weight: 8.9990 chunk 19 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 14 optimal weight: 0.0000 overall best weight: 0.3182 ------------------------------------------------------------------------------- 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 = 0.3450 r_free = 0.3450 target = 0.126752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.094742 restraints weight = 5072.801| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.44 r_work: 0.2908 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4128 Z= 0.146 Angle : 0.517 5.749 5632 Z= 0.259 Chirality : 0.043 0.156 634 Planarity : 0.005 0.043 705 Dihedral : 9.004 62.664 594 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 1.92 % Allowed : 6.73 % Favored : 91.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.39), residues: 506 helix: 1.12 (0.34), residues: 232 sheet: 0.06 (0.66), residues: 70 loop : -0.80 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.001 0.001 HIS A 425 PHE 0.011 0.001 PHE A 174 TYR 0.006 0.001 TYR A 104 ARG 0.001 0.000 ARG A 467 *********************** 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 57 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.440 Fit side-chains REVERT: A 19 LEU cc_start: 0.6786 (mt) cc_final: 0.6544 (tp) REVERT: A 238 ASP cc_start: 0.8421 (m-30) cc_final: 0.7931 (m-30) REVERT: A 247 LYS cc_start: 0.8577 (ttpp) cc_final: 0.8305 (ttmm) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.1268 time to fit residues: 9.1071 Evaluate side-chains 52 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 45 time to evaluate : 0.459 ------------------------------------------------------------------------------- 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 319 LEU 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 41 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.122163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.090399 restraints weight = 5099.566| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.41 r_work: 0.2851 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1741 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= 0.224 Angle : 0.538 5.813 5632 Z= 0.270 Chirality : 0.044 0.164 634 Planarity : 0.005 0.044 705 Dihedral : 8.716 65.178 594 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.40 % Allowed : 7.45 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.39), residues: 506 helix: 1.19 (0.34), residues: 232 sheet: -0.27 (0.64), residues: 76 loop : -0.83 (0.49), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.013 0.001 PHE A 174 TYR 0.010 0.001 TYR A 104 ARG 0.001 0.000 ARG A 367 *********************** 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 54 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.468 Fit side-chains REVERT: A 238 ASP cc_start: 0.8426 (m-30) cc_final: 0.7917 (m-30) REVERT: A 247 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8321 (ttmm) outliers start: 10 outliers final: 8 residues processed: 50 average time/residue: 0.1270 time to fit residues: 8.7715 Evaluate side-chains 50 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 ILE 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 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 34 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 14 optimal weight: 0.0980 chunk 27 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 37 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 30 optimal weight: 0.4980 chunk 20 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3425 r_free = 0.3425 target = 0.124085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.092609 restraints weight = 5159.401| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.43 r_work: 0.2888 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4128 Z= 0.161 Angle : 0.520 5.719 5632 Z= 0.260 Chirality : 0.043 0.157 634 Planarity : 0.005 0.044 705 Dihedral : 8.377 73.029 594 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 3.37 % Allowed : 7.21 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.40), residues: 506 helix: 1.41 (0.34), residues: 233 sheet: -0.27 (0.64), residues: 76 loop : -0.85 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 425 PHE 0.011 0.001 PHE A 500 TYR 0.008 0.001 TYR A 104 ARG 0.001 0.000 ARG A 397 *********************** 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 58 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.449 Fit side-chains REVERT: A 19 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6394 (tp) REVERT: A 238 ASP cc_start: 0.8479 (m-30) cc_final: 0.7973 (m-30) REVERT: A 247 LYS cc_start: 0.8560 (ttpp) cc_final: 0.8276 (ttmm) outliers start: 14 outliers final: 12 residues processed: 51 average time/residue: 0.1177 time to fit residues: 8.3005 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 ILE 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 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 32 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 41 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3444 r_free = 0.3444 target = 0.125394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.094271 restraints weight = 4974.481| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 2.36 r_work: 0.2921 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.1952 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= 0.179 Angle : 0.521 5.759 5632 Z= 0.260 Chirality : 0.043 0.156 634 Planarity : 0.005 0.044 705 Dihedral : 8.193 78.320 594 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.64 % Allowed : 8.17 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.40), residues: 506 helix: 1.53 (0.35), residues: 233 sheet: -0.28 (0.64), residues: 76 loop : -0.88 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.011 0.001 PHE A 500 TYR 0.009 0.001 TYR A 104 ARG 0.001 0.000 ARG A 367 *********************** 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 55 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.440 Fit side-chains REVERT: A 238 ASP cc_start: 0.8536 (m-30) cc_final: 0.8036 (m-30) REVERT: A 247 LYS cc_start: 0.8646 (ttpp) cc_final: 0.8353 (ttmm) outliers start: 11 outliers final: 11 residues processed: 50 average time/residue: 0.1397 time to fit residues: 9.7169 Evaluate side-chains 55 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 7 ILE 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 315 THR Chi-restraints excluded: chain A residue 371 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 23 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.3980 chunk 5 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.126634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.094942 restraints weight = 5043.596| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 2.39 r_work: 0.2930 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4128 Z= 0.182 Angle : 0.526 5.896 5632 Z= 0.262 Chirality : 0.043 0.156 634 Planarity : 0.005 0.045 705 Dihedral : 8.119 83.179 594 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.64 % Allowed : 8.65 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.40), residues: 506 helix: 1.59 (0.35), residues: 233 sheet: -0.21 (0.64), residues: 76 loop : -0.91 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.011 0.001 PHE A 500 TYR 0.009 0.001 TYR A 104 ARG 0.001 0.000 ARG A 123 *********************** 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 58 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.445 Fit side-chains REVERT: A 238 ASP cc_start: 0.8553 (m-30) cc_final: 0.8078 (m-30) REVERT: A 247 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8373 (ttmm) outliers start: 11 outliers final: 11 residues processed: 53 average time/residue: 0.1270 time to fit residues: 9.3049 Evaluate side-chains 56 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.451 ------------------------------------------------------------------------------- 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 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 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 35 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 30 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 12 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- 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 = 0.3476 r_free = 0.3476 target = 0.128255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.096525 restraints weight = 4913.030| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.40 r_work: 0.2946 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 4128 Z= 0.153 Angle : 0.517 5.716 5632 Z= 0.258 Chirality : 0.043 0.149 634 Planarity : 0.005 0.044 705 Dihedral : 8.007 88.853 594 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 2.64 % Allowed : 8.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.40), residues: 506 helix: 1.72 (0.35), residues: 233 sheet: -0.10 (0.64), residues: 76 loop : -0.90 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 34 HIS 0.001 0.000 HIS A 425 PHE 0.010 0.001 PHE A 500 TYR 0.008 0.001 TYR A 104 ARG 0.001 0.000 ARG A 397 *********************** 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: 11 poor density : 48 time to evaluate : 0.448 Fit side-chains REVERT: A 19 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6592 (tp) REVERT: A 85 MET cc_start: 0.8146 (mtm) cc_final: 0.7603 (ptp) REVERT: A 235 LEU cc_start: 0.8598 (tp) cc_final: 0.8382 (tp) REVERT: A 238 ASP cc_start: 0.8505 (m-30) cc_final: 0.8032 (m-30) REVERT: A 247 LYS cc_start: 0.8647 (ttpp) cc_final: 0.8356 (ttmm) outliers start: 11 outliers final: 10 residues processed: 54 average time/residue: 0.1212 time to fit residues: 9.1095 Evaluate side-chains 57 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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 5 optimal weight: 0.9980 chunk 11 optimal weight: 0.0470 chunk 16 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 0.2980 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 43 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3463 r_free = 0.3463 target = 0.126577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.096122 restraints weight = 4949.786| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.32 r_work: 0.2938 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4128 Z= 0.172 Angle : 0.529 5.736 5632 Z= 0.263 Chirality : 0.043 0.155 634 Planarity : 0.005 0.044 705 Dihedral : 7.841 86.846 594 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.40), residues: 506 helix: 1.77 (0.35), residues: 233 sheet: -0.03 (0.65), residues: 76 loop : -0.90 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.011 0.001 PHE A 500 TYR 0.009 0.001 TYR A 104 ARG 0.004 0.000 ARG A 332 *********************** 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 61 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.464 Fit side-chains REVERT: A 19 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6674 (tp) REVERT: A 85 MET cc_start: 0.8215 (mtm) cc_final: 0.7569 (ptp) REVERT: A 238 ASP cc_start: 0.8535 (m-30) cc_final: 0.8037 (m-30) REVERT: A 247 LYS cc_start: 0.8672 (ttpp) cc_final: 0.8369 (ttmm) outliers start: 12 outliers final: 11 residues processed: 54 average time/residue: 0.1335 time to fit residues: 10.0937 Evaluate side-chains 59 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.467 ------------------------------------------------------------------------------- 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 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 19 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 6.9990 chunk 38 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 34 optimal weight: 0.0070 chunk 49 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- 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 = 0.3452 r_free = 0.3452 target = 0.125995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.095535 restraints weight = 4996.368| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.32 r_work: 0.2938 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4128 Z= 0.177 Angle : 0.528 5.731 5632 Z= 0.263 Chirality : 0.043 0.152 634 Planarity : 0.005 0.044 705 Dihedral : 7.725 83.787 594 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.40), residues: 506 helix: 1.79 (0.35), residues: 233 sheet: -0.02 (0.65), residues: 76 loop : -0.93 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.011 0.001 PHE A 500 TYR 0.009 0.001 TYR A 104 ARG 0.003 0.000 ARG A 332 ********************** 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 61 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 49 time to evaluate : 0.397 Fit side-chains REVERT: A 19 LEU cc_start: 0.7219 (OUTLIER) cc_final: 0.6694 (tp) REVERT: A 85 MET cc_start: 0.8208 (mtm) cc_final: 0.7584 (ptp) REVERT: A 238 ASP cc_start: 0.8541 (m-30) cc_final: 0.8057 (m-30) REVERT: A 247 LYS cc_start: 0.8692 (ttpp) cc_final: 0.8389 (ttmm) outliers start: 12 outliers final: 11 residues processed: 54 average time/residue: 0.1213 time to fit residues: 8.9462 Evaluate side-chains 60 residues out of total 423 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 48 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 0.0980 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.126888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.095160 restraints weight = 4999.245| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.37 r_work: 0.2930 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4128 Z= 0.187 Angle : 0.534 6.081 5632 Z= 0.266 Chirality : 0.044 0.167 634 Planarity : 0.005 0.044 705 Dihedral : 7.626 80.726 594 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.88 % Allowed : 8.41 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.71 (0.40), residues: 506 helix: 1.79 (0.35), residues: 233 sheet: -0.01 (0.65), residues: 76 loop : -0.94 (0.48), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.001 0.000 HIS A 337 PHE 0.015 0.001 PHE A 465 TYR 0.009 0.001 TYR A 104 ARG 0.003 0.000 ARG A 332 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2383.92 seconds wall clock time: 41 minutes 31.59 seconds (2491.59 seconds total)