Starting phenix.real_space_refine on Wed Jun 4 15:03:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c03_16354/06_2025/8c03_16354.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c03_16354/06_2025/8c03_16354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c03_16354/06_2025/8c03_16354.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c03_16354/06_2025/8c03_16354.map" model { file = "/net/cci-nas-00/data/ceres_data/8c03_16354/06_2025/8c03_16354.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c03_16354/06_2025/8c03_16354.cif" } resolution = 3.89 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= 0.001 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 26 5.16 5 C 2187 2.51 5 N 542 2.21 5 O 574 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3330 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3300 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 9, 'TRANS': 419} Chain breaks: 2 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'SZU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.73, per 1000 atoms: 0.82 Number of scatterers: 3330 At special positions: 0 Unit cell: (78.12, 67.704, 84.63, 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 26 16.00 F 1 9.00 O 574 8.00 N 542 7.00 C 2187 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: 0.86 Conformation dependent library (CDL) restraints added in 394.1 milliseconds 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 92.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 23 through 54 removed outlier: 3.767A pdb=" N GLY A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 86 removed outlier: 3.634A pdb=" N GLY A 70 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N SER A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ASP A 84 " --> pdb=" O GLY A 80 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LYS A 85 " --> pdb=" O ASP A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.782A pdb=" N ALA A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 121 removed outlier: 3.723A pdb=" N LEU A 121 " --> pdb=" O LYS A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 156 removed outlier: 3.826A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 removed outlier: 3.742A pdb=" N GLY A 206 " --> pdb=" O VAL A 202 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ILE A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N SER A 209 " --> pdb=" O CYS A 205 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N THR A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 234 Processing helix chain 'A' and resid 288 through 305 Processing helix chain 'A' and resid 307 through 319 Processing helix chain 'A' and resid 325 through 336 Processing helix chain 'A' and resid 338 through 367 Processing helix chain 'A' and resid 369 through 393 Processing helix chain 'A' and resid 451 through 483 Processing helix chain 'A' and resid 485 through 487 No H-bonds generated for 'chain 'A' and resid 485 through 487' Processing helix chain 'A' and resid 488 through 514 removed outlier: 3.815A pdb=" N ASN A 493 " --> pdb=" O ARG A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 519 through 546 removed outlier: 4.118A pdb=" N LEU A 523 " --> pdb=" O ALA A 519 " (cutoff:3.500A) 308 hydrogen bonds defined for protein. 921 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.99 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1028 1.34 - 1.46: 824 1.46 - 1.58: 1505 1.58 - 1.70: 0 1.70 - 1.82: 44 Bond restraints: 3401 Sorted by residual: bond pdb=" C1 SZU A 601 " pdb=" C8 SZU A 601 " ideal model delta sigma weight residual 1.476 1.325 0.151 2.00e-02 2.50e+03 5.66e+01 bond pdb=" C2 SZU A 601 " pdb=" C3 SZU A 601 " ideal model delta sigma weight residual 1.517 1.377 0.140 2.00e-02 2.50e+03 4.92e+01 bond pdb=" C16 SZU A 601 " pdb=" C21 SZU A 601 " ideal model delta sigma weight residual 1.413 1.335 0.078 2.00e-02 2.50e+03 1.51e+01 bond pdb=" C8 SZU A 601 " pdb=" N6 SZU A 601 " ideal model delta sigma weight residual 1.396 1.329 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C20 SZU A 601 " pdb=" C21 SZU A 601 " ideal model delta sigma weight residual 1.395 1.328 0.067 2.00e-02 2.50e+03 1.11e+01 ... (remaining 3396 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 4565 2.51 - 5.03: 58 5.03 - 7.54: 2 7.54 - 10.06: 1 10.06 - 12.57: 1 Bond angle restraints: 4627 Sorted by residual: angle pdb=" C3 SZU A 601 " pdb=" C2 SZU A 601 " pdb=" N1 SZU A 601 " ideal model delta sigma weight residual 113.72 101.15 12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" N GLN A 496 " pdb=" CA GLN A 496 " pdb=" C GLN A 496 " ideal model delta sigma weight residual 111.36 106.91 4.45 1.09e+00 8.42e-01 1.67e+01 angle pdb=" N LEU A 59 " pdb=" CA LEU A 59 " pdb=" C LEU A 59 " ideal model delta sigma weight residual 111.11 106.50 4.61 1.20e+00 6.94e-01 1.48e+01 angle pdb=" CA THR A 334 " pdb=" C THR A 334 " pdb=" O THR A 334 " ideal model delta sigma weight residual 120.90 117.00 3.90 1.03e+00 9.43e-01 1.43e+01 angle pdb=" N PHE A 324 " pdb=" CA PHE A 324 " pdb=" C PHE A 324 " ideal model delta sigma weight residual 111.71 106.79 4.92 1.34e+00 5.57e-01 1.35e+01 ... (remaining 4622 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.30: 1769 14.30 - 28.61: 130 28.61 - 42.91: 44 42.91 - 57.21: 17 57.21 - 71.52: 6 Dihedral angle restraints: 1966 sinusoidal: 737 harmonic: 1229 Sorted by residual: dihedral pdb=" N GLU A 518 " pdb=" CA GLU A 518 " pdb=" CB GLU A 518 " pdb=" CG GLU A 518 " ideal model delta sinusoidal sigma weight residual -60.00 -119.88 59.88 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ILE A 186 " pdb=" CB ILE A 186 " pdb=" CG1 ILE A 186 " pdb=" CD1 ILE A 186 " ideal model delta sinusoidal sigma weight residual 180.00 123.89 56.11 3 1.50e+01 4.44e-03 9.38e+00 dihedral pdb=" N ILE A 78 " pdb=" CA ILE A 78 " pdb=" CB ILE A 78 " pdb=" CG1 ILE A 78 " ideal model delta sinusoidal sigma weight residual -60.00 -114.35 54.35 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 1963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 473 0.052 - 0.104: 74 0.104 - 0.156: 9 0.156 - 0.208: 3 0.208 - 0.260: 1 Chirality restraints: 560 Sorted by residual: chirality pdb=" CA LEU A 59 " pdb=" N LEU A 59 " pdb=" C LEU A 59 " pdb=" CB LEU A 59 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.69e+00 chirality pdb=" CA TYR A 333 " pdb=" N TYR A 333 " pdb=" C TYR A 333 " pdb=" CB TYR A 333 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.91e-01 chirality pdb=" CA PHE A 324 " pdb=" N PHE A 324 " pdb=" C PHE A 324 " pdb=" CB PHE A 324 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 6.98e-01 ... (remaining 557 not shown) Planarity restraints: 556 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 53 " -0.008 2.00e-02 2.50e+03 1.69e-02 2.86e+00 pdb=" C LEU A 53 " 0.029 2.00e-02 2.50e+03 pdb=" O LEU A 53 " -0.011 2.00e-02 2.50e+03 pdb=" N TYR A 54 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 324 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.75e+00 pdb=" C PHE A 324 " -0.029 2.00e-02 2.50e+03 pdb=" O PHE A 324 " 0.011 2.00e-02 2.50e+03 pdb=" N ASP A 325 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 SZU A 601 " -0.004 2.00e-02 2.50e+03 1.42e-02 2.53e+00 pdb=" C2 SZU A 601 " 0.016 2.00e-02 2.50e+03 pdb=" C8 SZU A 601 " 0.013 2.00e-02 2.50e+03 pdb=" N1 SZU A 601 " -0.023 2.00e-02 2.50e+03 pdb=" O1 SZU A 601 " -0.002 2.00e-02 2.50e+03 ... (remaining 553 not shown) Histogram of nonbonded interaction distances: 1.23 - 1.97: 1 1.97 - 2.70: 81 2.70 - 3.43: 5414 3.43 - 4.17: 7309 4.17 - 4.90: 13846 Nonbonded interactions: 26651 Sorted by model distance: nonbonded pdb=" OH TYR A 302 " pdb=" OE1 GLN A 496 " model vdw 1.232 3.040 nonbonded pdb=" CD1 LEU A 469 " pdb=" F1 SZU A 601 " model vdw 2.141 3.410 nonbonded pdb=" O TYR A 20 " pdb=" OG SER A 23 " model vdw 2.205 3.040 nonbonded pdb=" O ASN A 86 " pdb=" NZ LYS A 236 " model vdw 2.209 3.120 nonbonded pdb=" O LEU A 369 " pdb=" OG1 THR A 372 " model vdw 2.260 3.040 ... (remaining 26646 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 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 : 0.006 0.151 3401 Z= 0.345 Angle : 0.670 12.575 4627 Z= 0.403 Chirality : 0.040 0.260 560 Planarity : 0.003 0.017 556 Dihedral : 13.116 71.516 1178 Min Nonbonded Distance : 1.232 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 3.06 % Allowed : 8.08 % Favored : 88.86 % 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: 2.75 (0.41), residues: 423 helix: 2.29 (0.26), residues: 357 sheet: None (None), residues: 0 loop : -0.88 (0.85), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 470 HIS 0.003 0.001 HIS A 32 PHE 0.008 0.001 PHE A 508 TYR 0.006 0.001 TYR A 220 ARG 0.001 0.000 ARG A 88 Details of bonding type rmsd hydrogen bonds : bond 0.13852 ( 308) hydrogen bonds : angle 5.29252 ( 921) covalent geometry : bond 0.00607 ( 3401) covalent geometry : angle 0.67009 ( 4627) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 90 LYS cc_start: 0.7974 (tptt) cc_final: 0.7485 (tppt) REVERT: A 100 ASN cc_start: 0.7632 (m-40) cc_final: 0.6460 (m-40) REVERT: A 216 MET cc_start: 0.8280 (tpt) cc_final: 0.7925 (tpp) REVERT: A 319 MET cc_start: 0.7296 (ttt) cc_final: 0.6959 (tmm) outliers start: 11 outliers final: 3 residues processed: 138 average time/residue: 0.1499 time to fit residues: 25.5011 Evaluate side-chains 104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 174 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 21 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 125 HIS A 194 GLN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.177420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.142797 restraints weight = 4819.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.147299 restraints weight = 3035.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.149939 restraints weight = 2308.213| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.158 Angle : 0.580 6.753 4627 Z= 0.300 Chirality : 0.039 0.135 560 Planarity : 0.004 0.028 556 Dihedral : 7.431 75.543 476 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.62 % Allowed : 18.11 % Favored : 78.27 % 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: 3.07 (0.40), residues: 423 helix: 2.31 (0.25), residues: 371 sheet: None (None), residues: 0 loop : -0.08 (1.04), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.003 0.001 HIS A 32 PHE 0.026 0.002 PHE A 308 TYR 0.013 0.002 TYR A 29 ARG 0.008 0.001 ARG A 293 Details of bonding type rmsd hydrogen bonds : bond 0.05070 ( 308) hydrogen bonds : angle 4.32642 ( 921) covalent geometry : bond 0.00342 ( 3401) covalent geometry : angle 0.57953 ( 4627) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.326 Fit side-chains REVERT: A 90 LYS cc_start: 0.8068 (tptt) cc_final: 0.7514 (tppt) REVERT: A 166 ASP cc_start: 0.8256 (t0) cc_final: 0.7775 (t0) REVERT: A 173 MET cc_start: 0.7685 (ttm) cc_final: 0.7328 (ttm) REVERT: A 319 MET cc_start: 0.7569 (ttt) cc_final: 0.7114 (tmm) REVERT: A 366 LYS cc_start: 0.8339 (tptt) cc_final: 0.7831 (mmmt) REVERT: A 469 LEU cc_start: 0.8865 (tp) cc_final: 0.8623 (tp) outliers start: 13 outliers final: 4 residues processed: 113 average time/residue: 0.1293 time to fit residues: 18.0862 Evaluate side-chains 105 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 101 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 221 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 39 optimal weight: 8.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.173240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.137945 restraints weight = 4675.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142477 restraints weight = 2984.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.145506 restraints weight = 2281.138| |-----------------------------------------------------------------------------| r_work (final): 0.3685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3401 Z= 0.165 Angle : 0.596 6.603 4627 Z= 0.308 Chirality : 0.039 0.155 560 Planarity : 0.003 0.027 556 Dihedral : 6.925 73.251 470 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.34 % Allowed : 20.33 % Favored : 76.32 % 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: 2.88 (0.40), residues: 423 helix: 2.20 (0.25), residues: 371 sheet: None (None), residues: 0 loop : -0.21 (1.05), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 470 HIS 0.007 0.001 HIS A 43 PHE 0.022 0.002 PHE A 308 TYR 0.020 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04958 ( 308) hydrogen bonds : angle 4.27314 ( 921) covalent geometry : bond 0.00365 ( 3401) covalent geometry : angle 0.59561 ( 4627) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 103 time to evaluate : 0.333 Fit side-chains REVERT: A 57 SER cc_start: 0.8301 (m) cc_final: 0.7963 (p) REVERT: A 166 ASP cc_start: 0.8185 (t0) cc_final: 0.7720 (t0) REVERT: A 319 MET cc_start: 0.7772 (ttt) cc_final: 0.7217 (tmm) REVERT: A 366 LYS cc_start: 0.8409 (tptt) cc_final: 0.7940 (mmmt) REVERT: A 543 GLN cc_start: 0.7989 (mm110) cc_final: 0.7612 (mm-40) outliers start: 12 outliers final: 9 residues processed: 110 average time/residue: 0.1183 time to fit residues: 16.4340 Evaluate side-chains 107 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 98 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 5 optimal weight: 0.7980 chunk 6 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 39 optimal weight: 0.0370 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.0970 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 43 HIS ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.174974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.139839 restraints weight = 4802.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.144631 restraints weight = 2987.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147826 restraints weight = 2250.094| |-----------------------------------------------------------------------------| r_work (final): 0.3717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3401 Z= 0.140 Angle : 0.588 7.617 4627 Z= 0.300 Chirality : 0.039 0.147 560 Planarity : 0.003 0.033 556 Dihedral : 6.779 73.277 470 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 3.62 % Allowed : 20.89 % Favored : 75.49 % 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: 3.01 (0.40), residues: 423 helix: 2.31 (0.26), residues: 371 sheet: None (None), residues: 0 loop : -0.35 (1.02), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.008 0.002 HIS A 43 PHE 0.022 0.001 PHE A 308 TYR 0.028 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 308) hydrogen bonds : angle 4.14325 ( 921) covalent geometry : bond 0.00296 ( 3401) covalent geometry : angle 0.58833 ( 4627) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.365 Fit side-chains REVERT: A 166 ASP cc_start: 0.8130 (t0) cc_final: 0.7631 (t0) REVERT: A 319 MET cc_start: 0.7650 (ttt) cc_final: 0.7187 (tmm) REVERT: A 366 LYS cc_start: 0.8426 (tptt) cc_final: 0.8073 (tptt) outliers start: 13 outliers final: 9 residues processed: 110 average time/residue: 0.1240 time to fit residues: 17.1787 Evaluate side-chains 106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 30 optimal weight: 0.0870 chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 125 HIS A 212 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142160 restraints weight = 4831.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.146655 restraints weight = 3051.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.149706 restraints weight = 2314.703| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3401 Z= 0.148 Angle : 0.616 7.431 4627 Z= 0.309 Chirality : 0.039 0.181 560 Planarity : 0.003 0.032 556 Dihedral : 6.714 72.425 470 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.01 % Allowed : 23.40 % Favored : 71.59 % 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: 2.86 (0.40), residues: 423 helix: 2.19 (0.25), residues: 373 sheet: None (None), residues: 0 loop : -0.35 (1.02), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 42 HIS 0.006 0.002 HIS A 535 PHE 0.036 0.002 PHE A 308 TYR 0.022 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 308) hydrogen bonds : angle 4.14867 ( 921) covalent geometry : bond 0.00327 ( 3401) covalent geometry : angle 0.61645 ( 4627) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.395 Fit side-chains REVERT: A 166 ASP cc_start: 0.8048 (t0) cc_final: 0.7554 (t0) REVERT: A 319 MET cc_start: 0.7655 (ttt) cc_final: 0.7164 (tmm) REVERT: A 366 LYS cc_start: 0.8407 (tptt) cc_final: 0.8200 (tptt) REVERT: A 504 ASP cc_start: 0.7979 (t70) cc_final: 0.7611 (t0) outliers start: 18 outliers final: 14 residues processed: 103 average time/residue: 0.1293 time to fit residues: 16.9681 Evaluate side-chains 109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 212 ASN Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS A 212 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.176545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.141262 restraints weight = 4866.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.145915 restraints weight = 3072.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.149011 restraints weight = 2337.960| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3401 Z= 0.155 Angle : 0.626 8.333 4627 Z= 0.317 Chirality : 0.040 0.177 560 Planarity : 0.003 0.031 556 Dihedral : 6.652 71.264 470 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 11.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.01 % Allowed : 23.68 % Favored : 71.31 % 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: 2.87 (0.40), residues: 423 helix: 2.18 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.21 (1.02), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 470 HIS 0.004 0.001 HIS A 535 PHE 0.026 0.002 PHE A 308 TYR 0.022 0.002 TYR A 29 ARG 0.002 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04704 ( 308) hydrogen bonds : angle 4.18118 ( 921) covalent geometry : bond 0.00343 ( 3401) covalent geometry : angle 0.62570 ( 4627) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.396 Fit side-chains REVERT: A 166 ASP cc_start: 0.8113 (t0) cc_final: 0.7612 (t0) REVERT: A 319 MET cc_start: 0.7746 (ttt) cc_final: 0.7205 (tmm) REVERT: A 366 LYS cc_start: 0.8442 (tptt) cc_final: 0.8231 (tptt) REVERT: A 392 PHE cc_start: 0.8314 (t80) cc_final: 0.8026 (t80) REVERT: A 504 ASP cc_start: 0.8002 (t70) cc_final: 0.7632 (t0) outliers start: 18 outliers final: 15 residues processed: 103 average time/residue: 0.1215 time to fit residues: 15.9379 Evaluate side-chains 106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.176617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.141588 restraints weight = 4774.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.146247 restraints weight = 3020.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.149332 restraints weight = 2287.477| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3401 Z= 0.154 Angle : 0.617 8.773 4627 Z= 0.312 Chirality : 0.039 0.180 560 Planarity : 0.003 0.030 556 Dihedral : 6.568 69.883 470 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 5.01 % Allowed : 23.12 % Favored : 71.87 % 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: 2.90 (0.40), residues: 423 helix: 2.20 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.25 (1.02), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.004 0.001 HIS A 535 PHE 0.021 0.002 PHE A 308 TYR 0.020 0.002 TYR A 29 ARG 0.001 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04729 ( 308) hydrogen bonds : angle 4.16589 ( 921) covalent geometry : bond 0.00343 ( 3401) covalent geometry : angle 0.61678 ( 4627) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 94 time to evaluate : 0.369 Fit side-chains REVERT: A 202 VAL cc_start: 0.8559 (m) cc_final: 0.8317 (p) REVERT: A 319 MET cc_start: 0.7758 (ttt) cc_final: 0.7260 (tmm) REVERT: A 366 LYS cc_start: 0.8438 (tptt) cc_final: 0.8224 (tptt) REVERT: A 392 PHE cc_start: 0.8277 (t80) cc_final: 0.7998 (t80) REVERT: A 499 MET cc_start: 0.8624 (ttp) cc_final: 0.8387 (ttp) REVERT: A 504 ASP cc_start: 0.8013 (t70) cc_final: 0.7648 (t0) outliers start: 18 outliers final: 16 residues processed: 104 average time/residue: 0.1226 time to fit residues: 16.2033 Evaluate side-chains 110 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 5 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 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 = 0.4073 r_free = 0.4073 target = 0.176317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141481 restraints weight = 4705.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145969 restraints weight = 3017.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.148933 restraints weight = 2309.656| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.151 Angle : 0.620 9.412 4627 Z= 0.313 Chirality : 0.039 0.178 560 Planarity : 0.003 0.030 556 Dihedral : 6.500 68.665 470 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 4.74 % Allowed : 24.51 % Favored : 70.75 % 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: 2.95 (0.40), residues: 423 helix: 2.25 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.31 (1.00), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.004 0.001 HIS A 535 PHE 0.027 0.002 PHE A 308 TYR 0.020 0.001 TYR A 29 ARG 0.001 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 308) hydrogen bonds : angle 4.13455 ( 921) covalent geometry : bond 0.00336 ( 3401) covalent geometry : angle 0.62019 ( 4627) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.378 Fit side-chains REVERT: A 145 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8339 (mp) REVERT: A 166 ASP cc_start: 0.8068 (t0) cc_final: 0.7603 (t0) REVERT: A 202 VAL cc_start: 0.8509 (m) cc_final: 0.8276 (p) REVERT: A 319 MET cc_start: 0.7742 (ttt) cc_final: 0.7245 (tmm) REVERT: A 366 LYS cc_start: 0.8453 (tptt) cc_final: 0.8245 (tptt) REVERT: A 392 PHE cc_start: 0.8298 (t80) cc_final: 0.8022 (t80) REVERT: A 504 ASP cc_start: 0.8016 (t70) cc_final: 0.7651 (t0) outliers start: 17 outliers final: 14 residues processed: 107 average time/residue: 0.1248 time to fit residues: 17.1847 Evaluate side-chains 109 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 HIS ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.176426 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.141147 restraints weight = 4761.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.145544 restraints weight = 3076.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148652 restraints weight = 2375.370| |-----------------------------------------------------------------------------| r_work (final): 0.3709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3401 Z= 0.154 Angle : 0.633 9.541 4627 Z= 0.316 Chirality : 0.040 0.181 560 Planarity : 0.003 0.030 556 Dihedral : 6.409 66.097 470 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 5.01 % Allowed : 25.07 % Favored : 69.92 % 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: 2.99 (0.40), residues: 423 helix: 2.28 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.37 (0.98), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.004 0.001 HIS A 535 PHE 0.024 0.002 PHE A 308 TYR 0.019 0.001 TYR A 29 ARG 0.002 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 308) hydrogen bonds : angle 4.12705 ( 921) covalent geometry : bond 0.00345 ( 3401) covalent geometry : angle 0.63278 ( 4627) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 95 time to evaluate : 0.290 Fit side-chains REVERT: A 145 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8373 (mp) REVERT: A 202 VAL cc_start: 0.8404 (m) cc_final: 0.8190 (p) REVERT: A 319 MET cc_start: 0.7566 (ttt) cc_final: 0.7075 (tmm) REVERT: A 392 PHE cc_start: 0.8234 (t80) cc_final: 0.7964 (t80) REVERT: A 499 MET cc_start: 0.8634 (ttp) cc_final: 0.8405 (ttp) REVERT: A 504 ASP cc_start: 0.8031 (t70) cc_final: 0.7663 (t0) outliers start: 18 outliers final: 15 residues processed: 106 average time/residue: 0.1344 time to fit residues: 18.0469 Evaluate side-chains 108 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 38 optimal weight: 1.9990 chunk 30 optimal weight: 0.0020 chunk 2 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 40 optimal weight: 0.4980 chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 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 = 0.4092 r_free = 0.4092 target = 0.177645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.142266 restraints weight = 4763.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.146737 restraints weight = 3070.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.149871 restraints weight = 2353.676| |-----------------------------------------------------------------------------| r_work (final): 0.3735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3401 Z= 0.153 Angle : 0.690 10.543 4627 Z= 0.342 Chirality : 0.041 0.196 560 Planarity : 0.004 0.031 556 Dihedral : 6.429 65.260 470 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 4.18 % Allowed : 27.02 % Favored : 68.80 % 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: 2.87 (0.40), residues: 423 helix: 2.18 (0.26), residues: 374 sheet: None (None), residues: 0 loop : -0.30 (1.00), residues: 49 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.003 0.001 HIS A 535 PHE 0.027 0.002 PHE A 308 TYR 0.021 0.001 TYR A 29 ARG 0.004 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.04737 ( 308) hydrogen bonds : angle 4.17434 ( 921) covalent geometry : bond 0.00341 ( 3401) covalent geometry : angle 0.68957 ( 4627) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 846 Ramachandran restraints generated. 423 Oldfield, 0 Emsley, 423 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.326 Fit side-chains REVERT: A 145 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8394 (mp) REVERT: A 166 ASP cc_start: 0.8145 (t0) cc_final: 0.7741 (t0) REVERT: A 319 MET cc_start: 0.7534 (ttt) cc_final: 0.7038 (tmm) REVERT: A 366 LYS cc_start: 0.8370 (tptt) cc_final: 0.8092 (mmmt) REVERT: A 392 PHE cc_start: 0.8264 (t80) cc_final: 0.7996 (t80) REVERT: A 504 ASP cc_start: 0.8004 (t70) cc_final: 0.7623 (t0) outliers start: 15 outliers final: 12 residues processed: 98 average time/residue: 0.1219 time to fit residues: 15.1600 Evaluate side-chains 104 residues out of total 359 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 145 LEU Chi-restraints excluded: chain A residue 174 ASN Chi-restraints excluded: chain A residue 208 ILE Chi-restraints excluded: chain A residue 209 SER Chi-restraints excluded: chain A residue 221 VAL Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 389 ILE Chi-restraints excluded: chain A residue 458 LEU Chi-restraints excluded: chain A residue 475 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 6 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 chunk 37 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 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 = 0.4095 r_free = 0.4095 target = 0.178173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.143219 restraints weight = 4790.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.147594 restraints weight = 3064.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.150799 restraints weight = 2357.103| |-----------------------------------------------------------------------------| r_work (final): 0.3740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3401 Z= 0.157 Angle : 0.694 10.566 4627 Z= 0.345 Chirality : 0.042 0.193 560 Planarity : 0.004 0.030 556 Dihedral : 6.345 63.392 470 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 3.62 % Allowed : 28.69 % Favored : 67.69 % 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: 2.82 (0.40), residues: 423 helix: 2.16 (0.26), residues: 373 sheet: None (None), residues: 0 loop : -0.34 (0.99), residues: 50 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 82 HIS 0.003 0.001 HIS A 535 PHE 0.028 0.002 PHE A 292 TYR 0.011 0.001 TYR A 29 ARG 0.003 0.000 ARG A 179 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 308) hydrogen bonds : angle 4.23164 ( 921) covalent geometry : bond 0.00353 ( 3401) covalent geometry : angle 0.69387 ( 4627) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1402.26 seconds wall clock time: 25 minutes 16.12 seconds (1516.12 seconds total)