Starting phenix.real_space_refine on Mon Mar 11 09:25:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0m_15788/03_2024/8b0m_15788_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0m_15788/03_2024/8b0m_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0m_15788/03_2024/8b0m_15788.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0m_15788/03_2024/8b0m_15788.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0m_15788/03_2024/8b0m_15788_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b0m_15788/03_2024/8b0m_15788_updated.pdb" } 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 Residue "A PHE 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 468": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4015 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 4015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4015 Unusual residues: {'PTY': 1} Classifications: {'peptide': 508, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 36, 'TRANS': 471, None: 1} Not linked: pdbres="GLN A 509 " pdbres="PTY A 601 " 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 Time building chain proxies: 2.92, per 1000 atoms: 0.73 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 - 3.50 Amino acid : False - 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: 1.63 Conformation dependent library (CDL) restraints added in 754.3 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... running ksdssp... Secondary structure from input PDB file: 26 helices and 2 sheets defined 51.0% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 3 through 6 No H-bonds generated for 'chain 'A' and resid 3 through 6' Processing helix chain 'A' and resid 10 through 27 removed outlier: 3.652A pdb=" N GLY A 24 " --> pdb=" O PHE A 20 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N THR A 25 " --> pdb=" O GLY A 21 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N LEU A 26 " --> pdb=" O ALA A 22 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ALA A 27 " --> pdb=" O CYS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.784A pdb=" N ILE A 39 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N SER A 40 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA A 46 " --> pdb=" O GLY A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 68 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 80 removed outlier: 3.592A pdb=" N ALA A 80 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 115 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 121 through 125 Processing helix chain 'A' and resid 128 through 139 Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 151 through 156 removed outlier: 3.859A pdb=" N GLN A 155 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ILE A 156 " --> pdb=" O GLY A 152 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 151 through 156' Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 164 through 167 No H-bonds generated for 'chain 'A' and resid 164 through 167' Processing helix chain 'A' and resid 169 through 188 Processing helix chain 'A' and resid 193 through 210 removed outlier: 3.965A pdb=" N PHE A 202 " --> pdb=" O ALA A 198 " (cutoff:3.500A) Proline residue: A 205 - end of helix removed outlier: 4.588A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG A 209 " --> pdb=" O PRO A 205 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR A 210 " --> pdb=" O PHE A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 235 No H-bonds generated for 'chain 'A' and resid 233 through 235' Processing helix chain 'A' and resid 239 through 256 removed outlier: 4.572A pdb=" N LEU A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN A 244 " --> pdb=" O GLY A 240 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 278 through 291 Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 351 through 354 No H-bonds generated for 'chain 'A' and resid 351 through 354' Processing helix chain 'A' and resid 356 through 358 No H-bonds generated for 'chain 'A' and resid 356 through 358' Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 393 through 399 Processing helix chain 'A' and resid 413 through 416 Processing helix chain 'A' and resid 421 through 436 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 482 through 486 Processing helix chain 'A' and resid 489 through 507 removed outlier: 4.087A pdb=" N MET A 505 " --> pdb=" O ALA A 501 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 468 through 474 removed outlier: 4.136A pdb=" N LEU A 262 " --> pdb=" O GLN A 223 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER A 294 " --> pdb=" O ILE A 263 " (cutoff:3.500A) removed outlier: 7.957A pdb=" N TRP A 265 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N VAL A 296 " --> pdb=" O TRP A 265 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 375 through 377 removed outlier: 6.916A pdb=" N TYR A 406 " --> pdb=" O THR A 383 " (cutoff:3.500A) removed outlier: 7.601A pdb=" N THR A 409 " --> pdb=" O PRO A 439 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 441 " --> pdb=" O THR A 409 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N SER A 411 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N SER A 443 " --> pdb=" O SER A 411 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 460 " --> pdb=" O VAL A 451 " (cutoff:3.500A) 164 hydrogen bonds defined for protein. 435 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: 1.24 Time building geometry restraints manager: 1.77 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: 100.10 - 106.88: 182 106.88 - 113.65: 2254 113.65 - 120.42: 1544 120.42 - 127.20: 1584 127.20 - 133.97: 68 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: 943 2.79 - 3.31: 3908 3.31 - 3.84: 6801 3.84 - 4.37: 8520 4.37 - 4.90: 14428 Nonbonded interactions: 34600 Sorted by model distance: nonbonded pdb=" O VAL A 77 " pdb=" OG1 THR A 81 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR A 333 " pdb=" OE1 GLU A 389 " model vdw 2.269 2.440 nonbonded pdb=" OE1 GLU A 274 " pdb=" NH2 ARG A 332 " model vdw 2.303 2.520 nonbonded pdb=" O ALA A 98 " pdb=" OG SER A 102 " model vdw 2.327 2.440 nonbonded pdb=" OE1 GLU A 136 " pdb=" NH2 ARG A 139 " model vdw 2.344 2.520 ... (remaining 34595 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: 0.670 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: 3.080 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.280 Find NCS groups from input model: 0.110 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.120 ------------------------------------------------------------------------------- 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= 0.234 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 fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.462 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: 0.2009 time to fit residues: 17.8042 Evaluate side-chains 44 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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: 6.9990 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 39 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.1101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4128 Z= 0.261 Angle : 0.550 5.850 5632 Z= 0.275 Chirality : 0.044 0.175 634 Planarity : 0.005 0.040 705 Dihedral : 9.582 83.382 594 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.72 % Allowed : 7.69 % Favored : 91.59 % 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 (0.38), residues: 506 helix: 0.52 (0.33), residues: 230 sheet: 0.24 (0.72), residues: 63 loop : -0.86 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 63 HIS 0.002 0.001 HIS A 425 PHE 0.017 0.001 PHE A 500 TYR 0.009 0.001 TYR A 31 ARG 0.001 0.000 ARG A 123 *********************** 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 fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.500 Fit side-chains REVERT: A 19 LEU cc_start: 0.6907 (mt) cc_final: 0.6576 (tp) REVERT: A 238 ASP cc_start: 0.8458 (m-30) cc_final: 0.8046 (m-30) REVERT: A 247 LYS cc_start: 0.8673 (ttpp) cc_final: 0.8377 (ttmm) outliers start: 3 outliers final: 3 residues processed: 48 average time/residue: 0.1758 time to fit residues: 10.7296 Evaluate side-chains 40 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.418 ------------------------------------------------------------------------------- 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 25 optimal weight: 7.9990 chunk 14 optimal weight: 0.4980 chunk 37 optimal weight: 5.9990 chunk 30 optimal weight: 7.9990 chunk 12 optimal weight: 0.3980 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 0.5980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.1309 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= 0.190 Angle : 0.520 5.847 5632 Z= 0.257 Chirality : 0.043 0.164 634 Planarity : 0.005 0.041 705 Dihedral : 9.057 67.650 594 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.92 % Allowed : 7.45 % Favored : 90.62 % 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: -0.01 (0.39), residues: 506 helix: 0.74 (0.33), residues: 232 sheet: 0.43 (0.74), residues: 62 loop : -0.91 (0.46), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 34 HIS 0.001 0.001 HIS A 337 PHE 0.013 0.001 PHE A 174 TYR 0.007 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 48 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.434 Fit side-chains REVERT: A 19 LEU cc_start: 0.6808 (mt) cc_final: 0.6526 (tp) REVERT: A 238 ASP cc_start: 0.8497 (m-30) cc_final: 0.8048 (m-30) REVERT: A 247 LYS cc_start: 0.8685 (ttpp) cc_final: 0.8377 (ttmm) outliers start: 8 outliers final: 8 residues processed: 47 average time/residue: 0.1390 time to fit residues: 8.7484 Evaluate side-chains 46 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 38 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 6.9990 chunk 23 optimal weight: 0.0020 chunk 5 optimal weight: 0.0040 chunk 21 optimal weight: 4.9990 chunk 30 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 overall best weight: 0.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4128 Z= 0.172 Angle : 0.501 5.811 5632 Z= 0.247 Chirality : 0.043 0.158 634 Planarity : 0.005 0.042 705 Dihedral : 8.628 88.604 594 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.68 % Allowed : 8.89 % 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: 0.24 (0.39), residues: 506 helix: 1.05 (0.34), residues: 231 sheet: 0.50 (0.74), residues: 62 loop : -0.91 (0.45), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.012 0.001 PHE A 500 TYR 0.007 0.001 TYR A 104 ARG 0.001 0.000 ARG A 123 *********************** 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 51 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.418 Fit side-chains REVERT: A 238 ASP cc_start: 0.8503 (m-30) cc_final: 0.8091 (m-30) REVERT: A 247 LYS cc_start: 0.8648 (ttpp) cc_final: 0.8330 (ttmm) outliers start: 7 outliers final: 6 residues processed: 49 average time/residue: 0.1256 time to fit residues: 8.4102 Evaluate side-chains 45 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 39 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 19 optimal weight: 0.8980 chunk 41 optimal weight: 0.0010 chunk 33 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.1556 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= 0.182 Angle : 0.510 5.810 5632 Z= 0.251 Chirality : 0.043 0.159 634 Planarity : 0.005 0.042 705 Dihedral : 8.219 81.486 594 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.92 % Allowed : 8.89 % 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: 0.35 (0.39), residues: 506 helix: 1.18 (0.34), residues: 231 sheet: 0.51 (0.74), residues: 62 loop : -0.87 (0.46), residues: 213 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.001 0.001 HIS A 337 PHE 0.011 0.001 PHE A 500 TYR 0.008 0.001 TYR A 104 ARG 0.001 0.000 ARG A 367 *********************** 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 51 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.499 Fit side-chains REVERT: A 85 MET cc_start: 0.8393 (mtm) cc_final: 0.7703 (ptp) REVERT: A 238 ASP cc_start: 0.8496 (m-30) cc_final: 0.8092 (m-30) REVERT: A 239 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8219 (mm-30) REVERT: A 247 LYS cc_start: 0.8665 (ttpp) cc_final: 0.8341 (ttmm) outliers start: 8 outliers final: 8 residues processed: 48 average time/residue: 0.1335 time to fit residues: 8.7338 Evaluate side-chains 47 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR 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 11 optimal weight: 0.4980 chunk 48 optimal weight: 0.0370 chunk 40 optimal weight: 0.0970 chunk 22 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.4256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 GLN ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4128 Z= 0.149 Angle : 0.493 5.754 5632 Z= 0.242 Chirality : 0.042 0.150 634 Planarity : 0.005 0.043 705 Dihedral : 7.490 64.150 594 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.40 % Allowed : 8.89 % 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: 0.55 (0.40), residues: 506 helix: 1.40 (0.34), residues: 231 sheet: 0.33 (0.71), residues: 70 loop : -0.78 (0.48), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.001 HIS A 425 PHE 0.011 0.001 PHE A 500 TYR 0.006 0.001 TYR A 104 ARG 0.001 0.000 ARG A 13 *********************** 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 56 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 46 time to evaluate : 0.467 Fit side-chains REVERT: A 19 LEU cc_start: 0.6817 (OUTLIER) cc_final: 0.6314 (tp) REVERT: A 238 ASP cc_start: 0.8505 (m-30) cc_final: 0.8196 (m-30) REVERT: A 247 LYS cc_start: 0.8666 (ttpp) cc_final: 0.8339 (ttmm) outliers start: 10 outliers final: 8 residues processed: 52 average time/residue: 0.1436 time to fit residues: 9.9194 Evaluate side-chains 52 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 43 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 102 SER 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 27 optimal weight: 7.9990 chunk 40 optimal weight: 0.0050 chunk 48 optimal weight: 0.5980 chunk 30 optimal weight: 5.9990 chunk 29 optimal weight: 0.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.1730 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= 0.176 Angle : 0.511 7.053 5632 Z= 0.248 Chirality : 0.043 0.155 634 Planarity : 0.005 0.043 705 Dihedral : 7.255 57.380 594 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % 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: 0.53 (0.40), residues: 506 helix: 1.40 (0.34), residues: 231 sheet: 0.28 (0.71), residues: 70 loop : -0.81 (0.48), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.011 0.001 PHE A 500 TYR 0.008 0.001 TYR A 104 ARG 0.004 0.000 ARG A 303 *********************** 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 54 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 43 time to evaluate : 0.466 Fit side-chains REVERT: A 19 LEU cc_start: 0.6860 (OUTLIER) cc_final: 0.6354 (tp) REVERT: A 85 MET cc_start: 0.8414 (mtm) cc_final: 0.7977 (ptp) REVERT: A 238 ASP cc_start: 0.8448 (m-30) cc_final: 0.8168 (m-30) REVERT: A 247 LYS cc_start: 0.8709 (ttpp) cc_final: 0.8387 (ttmm) outliers start: 11 outliers final: 9 residues processed: 51 average time/residue: 0.1294 time to fit residues: 9.0498 Evaluate side-chains 52 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 102 SER Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 260 SER Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 371 ILE Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 500 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.0000 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.1726 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= 0.187 Angle : 0.514 6.963 5632 Z= 0.251 Chirality : 0.043 0.155 634 Planarity : 0.005 0.043 705 Dihedral : 7.080 56.721 594 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % 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: 0.50 (0.39), residues: 506 helix: 1.41 (0.34), residues: 231 sheet: 0.28 (0.71), residues: 70 loop : -0.87 (0.47), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 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 303 *********************** 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 58 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 46 time to evaluate : 0.452 Fit side-chains REVERT: A 19 LEU cc_start: 0.6880 (OUTLIER) cc_final: 0.6369 (tp) REVERT: A 85 MET cc_start: 0.8442 (mtm) cc_final: 0.7948 (ptp) REVERT: A 238 ASP cc_start: 0.8378 (m-30) cc_final: 0.8097 (m-30) REVERT: A 239 GLU cc_start: 0.8331 (mm-30) cc_final: 0.8114 (mm-30) REVERT: A 247 LYS cc_start: 0.8712 (ttpp) cc_final: 0.8388 (ttmm) outliers start: 12 outliers final: 9 residues processed: 54 average time/residue: 0.1285 time to fit residues: 9.4320 Evaluate side-chains 52 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 102 SER 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 40 optimal weight: 0.6980 chunk 42 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.1785 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= 0.183 Angle : 0.513 6.662 5632 Z= 0.250 Chirality : 0.043 0.159 634 Planarity : 0.005 0.044 705 Dihedral : 6.912 57.037 594 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 2.40 % Allowed : 8.17 % 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: 0.50 (0.40), residues: 506 helix: 1.45 (0.34), residues: 231 sheet: 0.04 (0.69), residues: 76 loop : -0.85 (0.48), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.012 0.001 PHE A 500 TYR 0.009 0.001 TYR A 104 ARG 0.004 0.000 ARG A 303 *********************** 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 55 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 45 time to evaluate : 0.456 Fit side-chains REVERT: A 19 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6367 (tp) REVERT: A 85 MET cc_start: 0.8417 (mtm) cc_final: 0.8026 (ptp) REVERT: A 238 ASP cc_start: 0.8352 (m-30) cc_final: 0.8055 (m-30) REVERT: A 239 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8118 (mm-30) REVERT: A 247 LYS cc_start: 0.8689 (ttpp) cc_final: 0.8374 (ttmm) outliers start: 10 outliers final: 9 residues processed: 52 average time/residue: 0.1421 time to fit residues: 9.7819 Evaluate side-chains 52 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 102 SER 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 4 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 24 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 39 optimal weight: 0.0970 chunk 16 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4128 Z= 0.157 Angle : 0.505 6.501 5632 Z= 0.246 Chirality : 0.042 0.149 634 Planarity : 0.005 0.043 705 Dihedral : 6.756 55.913 594 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.40 % Allowed : 8.17 % 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: 0.58 (0.40), residues: 506 helix: 1.55 (0.34), residues: 231 sheet: 0.07 (0.69), residues: 76 loop : -0.85 (0.48), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.000 HIS A 337 PHE 0.011 0.001 PHE A 500 TYR 0.007 0.001 TYR A 104 ARG 0.005 0.000 ARG A 303 ********************** 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 53 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.470 Fit side-chains REVERT: A 19 LEU cc_start: 0.6853 (OUTLIER) cc_final: 0.6338 (tp) REVERT: A 85 MET cc_start: 0.8384 (mtm) cc_final: 0.8043 (ptp) REVERT: A 238 ASP cc_start: 0.8337 (m-30) cc_final: 0.8040 (m-30) REVERT: A 247 LYS cc_start: 0.8688 (ttpp) cc_final: 0.8368 (ttmm) REVERT: A 303 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7759 (tpp80) outliers start: 10 outliers final: 9 residues processed: 50 average time/residue: 0.1476 time to fit residues: 9.7803 Evaluate side-chains 53 residues out of total 423 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 43 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 LEU Chi-restraints excluded: chain A residue 31 TYR Chi-restraints excluded: chain A residue 102 SER 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 40 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 chunk 2 optimal weight: 0.0470 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.0040 chunk 26 optimal weight: 0.4980 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 overall best weight: 0.2628 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.129789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.098718 restraints weight = 4956.995| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 2.41 r_work: 0.2970 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.2023 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= 0.130 Angle : 0.492 6.302 5632 Z= 0.239 Chirality : 0.042 0.162 634 Planarity : 0.005 0.044 705 Dihedral : 6.414 55.368 594 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.40 % Allowed : 8.41 % 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: 0.78 (0.40), residues: 506 helix: 1.70 (0.34), residues: 232 sheet: 0.38 (0.73), residues: 70 loop : -0.79 (0.48), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 489 HIS 0.001 0.001 HIS A 337 PHE 0.010 0.001 PHE A 500 TYR 0.005 0.001 TYR A 406 ARG 0.004 0.000 ARG A 303 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1386.44 seconds wall clock time: 25 minutes 28.02 seconds (1528.02 seconds total)