Starting phenix.real_space_refine on Wed Jul 23 12:28:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws7_37800/07_2025/8ws7_37800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws7_37800/07_2025/8ws7_37800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ws7_37800/07_2025/8ws7_37800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws7_37800/07_2025/8ws7_37800.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws7_37800/07_2025/8ws7_37800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws7_37800/07_2025/8ws7_37800.cif" } resolution = 3.26 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= 0.015 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 P 54 5.49 5 S 3 5.16 5 C 1934 2.51 5 N 604 2.21 5 O 738 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3333 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2207 Classifications: {'peptide': 279} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 27, 'TRANS': 251} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 360 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "B" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 627 Classifications: {'RNA': 30} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 10, 'rna3p_pyr': 14} Link IDs: {'rna2p': 6, 'rna3p': 23} Chain: "D" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 139 Classifications: {'DNA': 7} Link IDs: {'rna3p': 6} Time building chain proxies: 4.99, per 1000 atoms: 1.50 Number of scatterers: 3333 At special positions: 0 Unit cell: (54.78, 77.88, 91.08, 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 3 16.00 P 54 15.00 O 738 8.00 N 604 7.00 C 1934 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: 2.30 Conformation dependent library (CDL) restraints added in 403.1 milliseconds 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 508 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 38.0% alpha, 7.9% beta 9 base pairs and 31 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 75 through 89 Processing helix chain 'A' and resid 92 through 99 removed outlier: 4.087A pdb=" N GLU A 97 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.654A pdb=" N PHE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 158 removed outlier: 3.582A pdb=" N ILE A 132 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 134 " --> pdb=" O ASN A 130 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N THR A 136 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N PHE A 137 " --> pdb=" O LEU A 133 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL A 143 " --> pdb=" O ARG A 139 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 3.534A pdb=" N ARG A 251 " --> pdb=" O GLU A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 292 removed outlier: 3.559A pdb=" N LEU A 290 " --> pdb=" O LYS A 286 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LYS A 291 " --> pdb=" O GLU A 287 " (cutoff:3.500A) removed outlier: 4.322A pdb=" N GLU A 292 " --> pdb=" O ALA A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 319 Processing helix chain 'A' and resid 327 through 332 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.684A pdb=" N ILE A 198 " --> pdb=" O LEU A 341 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N GLN A 68 " --> pdb=" O TRP A 304 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TRP A 304 " --> pdb=" O GLN A 68 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE A 296 " --> pdb=" O MET A 307 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 207 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 31 stacking parallelities Total time for adding SS restraints: 0.94 Time building geometry restraints manager: 1.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 774 1.33 - 1.45: 971 1.45 - 1.57: 1670 1.57 - 1.69: 105 1.69 - 1.81: 4 Bond restraints: 3524 Sorted by residual: bond pdb=" CA LYS A 273 " pdb=" C LYS A 273 " ideal model delta sigma weight residual 1.522 1.561 -0.039 1.06e-02 8.90e+03 1.33e+01 bond pdb=" CA ARG A 70 " pdb=" C ARG A 70 " ideal model delta sigma weight residual 1.519 1.547 -0.028 1.01e-02 9.80e+03 7.89e+00 bond pdb=" C ARG A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.330 1.363 -0.033 1.22e-02 6.72e+03 7.24e+00 bond pdb=" C LYS A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.333 1.366 -0.032 1.44e-02 4.82e+03 5.08e+00 bond pdb=" CA PHE A 335 " pdb=" C PHE A 335 " ideal model delta sigma weight residual 1.523 1.507 0.016 1.19e-02 7.06e+03 1.84e+00 ... (remaining 3519 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 4796 1.45 - 2.90: 185 2.90 - 4.35: 28 4.35 - 5.80: 4 5.80 - 7.25: 2 Bond angle restraints: 5015 Sorted by residual: angle pdb=" N LEU A 72 " pdb=" CA LEU A 72 " pdb=" C LEU A 72 " ideal model delta sigma weight residual 113.01 117.65 -4.64 1.20e+00 6.94e-01 1.50e+01 angle pdb=" C ARG A 70 " pdb=" CA ARG A 70 " pdb=" CB ARG A 70 " ideal model delta sigma weight residual 109.22 113.64 -4.42 1.52e+00 4.33e-01 8.47e+00 angle pdb=" CA SER A 69 " pdb=" C SER A 69 " pdb=" N ARG A 70 " ideal model delta sigma weight residual 117.17 114.05 3.12 1.18e+00 7.18e-01 6.97e+00 angle pdb=" O SER A 69 " pdb=" C SER A 69 " pdb=" N ARG A 70 " ideal model delta sigma weight residual 122.09 124.72 -2.63 1.08e+00 8.57e-01 5.92e+00 angle pdb=" N TYR A 140 " pdb=" CA TYR A 140 " pdb=" C TYR A 140 " ideal model delta sigma weight residual 111.07 108.81 2.26 1.07e+00 8.73e-01 4.46e+00 ... (remaining 5010 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.05: 1926 34.05 - 68.10: 172 68.10 - 102.14: 17 102.14 - 136.19: 0 136.19 - 170.24: 2 Dihedral angle restraints: 2117 sinusoidal: 1322 harmonic: 795 Sorted by residual: dihedral pdb=" O4' U B 10 " pdb=" C1' U B 10 " pdb=" N1 U B 10 " pdb=" C2 U B 10 " ideal model delta sinusoidal sigma weight residual 200.00 58.25 141.75 1 1.50e+01 4.44e-03 7.62e+01 dihedral pdb=" O4' U B -9 " pdb=" C1' U B -9 " pdb=" N1 U B -9 " pdb=" C2 U B -9 " ideal model delta sinusoidal sigma weight residual 232.00 61.76 170.24 1 1.70e+01 3.46e-03 6.60e+01 dihedral pdb=" CA TRP A 318 " pdb=" C TRP A 318 " pdb=" N ARG A 319 " pdb=" CA ARG A 319 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 ... (remaining 2114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 484 0.052 - 0.103: 62 0.103 - 0.155: 22 0.155 - 0.206: 1 0.206 - 0.258: 2 Chirality restraints: 571 Sorted by residual: chirality pdb=" CA LEU A 72 " pdb=" N LEU A 72 " pdb=" C LEU A 72 " pdb=" CB LEU A 72 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 198 " pdb=" N ILE A 198 " pdb=" C ILE A 198 " pdb=" CB ILE A 198 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA LYS A 273 " pdb=" N LYS A 273 " pdb=" C LYS A 273 " pdb=" CB LYS A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.92e-01 ... (remaining 568 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 70 " -0.040 5.00e-02 4.00e+02 6.19e-02 6.13e+00 pdb=" N PRO A 71 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 71 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 71 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER A 69 " 0.009 2.00e-02 2.50e+03 1.92e-02 3.68e+00 pdb=" C SER A 69 " -0.033 2.00e-02 2.50e+03 pdb=" O SER A 69 " 0.013 2.00e-02 2.50e+03 pdb=" N ARG A 70 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 75 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO A 76 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.025 5.00e-02 4.00e+02 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 809 2.80 - 3.32: 2904 3.32 - 3.85: 5913 3.85 - 4.37: 7050 4.37 - 4.90: 10629 Nonbonded interactions: 27305 Sorted by model distance: nonbonded pdb=" NE2 GLN A 127 " pdb=" O4 DT D -2 " model vdw 2.272 3.120 nonbonded pdb=" NH1 ARG A 260 " pdb=" O6 G B -16 " model vdw 2.314 3.120 nonbonded pdb=" O2' C B -6 " pdb=" OP2 C B -5 " model vdw 2.334 3.040 nonbonded pdb=" O6 DG C 5 " pdb=" N4 DC D -6 " model vdw 2.371 3.120 nonbonded pdb=" N6 DA C -10 " pdb=" O4 U B 10 " model vdw 2.425 3.120 ... (remaining 27300 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.630 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: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.940 Find NCS groups from input model: 0.020 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 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 : 0.004 0.039 3524 Z= 0.196 Angle : 0.646 7.250 5015 Z= 0.370 Chirality : 0.042 0.258 571 Planarity : 0.006 0.062 450 Dihedral : 21.449 170.241 1609 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.86 % Allowed : 1.72 % Favored : 97.41 % 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: -1.30 (0.50), residues: 275 helix: -1.23 (0.51), residues: 98 sheet: 0.58 (1.11), residues: 26 loop : -0.78 (0.50), residues: 151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 318 HIS 0.002 0.001 HIS A 253 PHE 0.009 0.001 PHE A 334 TYR 0.006 0.001 TYR A 201 ARG 0.004 0.000 ARG A 70 Details of bonding type rmsd hydrogen bonds : bond 0.25870 ( 94) hydrogen bonds : angle 9.73398 ( 247) covalent geometry : bond 0.00352 ( 3524) covalent geometry : angle 0.64627 ( 5015) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.258 Fit side-chains REVERT: A 74 GLU cc_start: 0.6449 (mp0) cc_final: 0.6114 (mp0) REVERT: A 302 LYS cc_start: 0.7975 (mtpp) cc_final: 0.7761 (mtpp) outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.3768 time to fit residues: 12.9815 Evaluate side-chains 26 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 26 optimal weight: 0.0370 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 14 optimal weight: 0.0020 chunk 18 optimal weight: 0.0970 chunk 28 optimal weight: 0.9990 overall best weight: 0.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.146073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.130648 restraints weight = 4833.578| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.33 r_work: 0.3548 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.1452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3524 Z= 0.131 Angle : 0.582 7.255 5015 Z= 0.308 Chirality : 0.038 0.138 571 Planarity : 0.005 0.034 450 Dihedral : 23.556 170.217 1055 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 0.43 % Allowed : 8.19 % Favored : 91.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.84 (0.49), residues: 275 helix: -0.65 (0.49), residues: 104 sheet: 0.42 (0.98), residues: 33 loop : -0.60 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 318 HIS 0.002 0.001 HIS A 214 PHE 0.008 0.001 PHE A 350 TYR 0.007 0.001 TYR A 201 ARG 0.003 0.000 ARG A 260 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 94) hydrogen bonds : angle 5.11157 ( 247) covalent geometry : bond 0.00283 ( 3524) covalent geometry : angle 0.58227 ( 5015) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.242 Fit side-chains REVERT: A 74 GLU cc_start: 0.6857 (mp0) cc_final: 0.6548 (mp0) REVERT: A 302 LYS cc_start: 0.8406 (mtpp) cc_final: 0.8184 (mtpp) outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.3236 time to fit residues: 11.3259 Evaluate side-chains 29 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 155 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 23 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.5980 chunk 25 optimal weight: 0.0070 chunk 2 optimal weight: 0.4980 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.127678 restraints weight = 4799.570| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 1.32 r_work: 0.3491 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.1877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3524 Z= 0.181 Angle : 0.622 8.030 5015 Z= 0.325 Chirality : 0.041 0.149 571 Planarity : 0.006 0.036 450 Dihedral : 23.435 169.616 1055 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.29 % Allowed : 9.91 % Favored : 88.79 % 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: -0.75 (0.50), residues: 275 helix: -0.45 (0.51), residues: 102 sheet: -0.09 (1.06), residues: 28 loop : -0.50 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 112 HIS 0.003 0.001 HIS A 214 PHE 0.013 0.002 PHE A 350 TYR 0.009 0.001 TYR A 201 ARG 0.005 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 94) hydrogen bonds : angle 4.83916 ( 247) covalent geometry : bond 0.00398 ( 3524) covalent geometry : angle 0.62169 ( 5015) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.249 Fit side-chains REVERT: A 74 GLU cc_start: 0.7076 (mp0) cc_final: 0.6575 (mp0) REVERT: A 109 LEU cc_start: 0.8121 (mt) cc_final: 0.7918 (mt) REVERT: A 190 GLU cc_start: 0.6835 (mp0) cc_final: 0.6264 (mp0) REVERT: A 302 LYS cc_start: 0.8531 (mtpp) cc_final: 0.8292 (mtpp) outliers start: 3 outliers final: 1 residues processed: 34 average time/residue: 0.3110 time to fit residues: 11.9448 Evaluate side-chains 32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** 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 = 0.3768 r_free = 0.3768 target = 0.139669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.123967 restraints weight = 4865.245| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.38 r_work: 0.3455 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3524 Z= 0.272 Angle : 0.684 6.938 5015 Z= 0.356 Chirality : 0.045 0.165 571 Planarity : 0.006 0.044 450 Dihedral : 23.547 169.558 1051 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 3.45 % Allowed : 10.78 % Favored : 85.78 % 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: -1.22 (0.48), residues: 275 helix: -0.69 (0.50), residues: 103 sheet: -0.65 (0.88), residues: 33 loop : -0.84 (0.50), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP A 112 HIS 0.004 0.002 HIS A 253 PHE 0.020 0.003 PHE A 350 TYR 0.013 0.002 TYR A 89 ARG 0.007 0.001 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04806 ( 94) hydrogen bonds : angle 4.92412 ( 247) covalent geometry : bond 0.00603 ( 3524) covalent geometry : angle 0.68375 ( 5015) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 28 time to evaluate : 0.263 Fit side-chains REVERT: A 302 LYS cc_start: 0.8604 (mtpp) cc_final: 0.8360 (mtpp) outliers start: 8 outliers final: 3 residues processed: 34 average time/residue: 0.2630 time to fit residues: 10.3646 Evaluate side-chains 32 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 17 optimal weight: 0.0010 chunk 10 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** 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 = 0.3805 r_free = 0.3805 target = 0.142189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.126513 restraints weight = 4883.277| |-----------------------------------------------------------------------------| r_work (start): 0.3587 rms_B_bonded: 1.31 r_work: 0.3496 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3524 Z= 0.167 Angle : 0.570 6.548 5015 Z= 0.302 Chirality : 0.039 0.145 571 Planarity : 0.005 0.041 450 Dihedral : 23.284 169.986 1051 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.88 % Allowed : 14.22 % Favored : 81.90 % 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: -0.89 (0.49), residues: 275 helix: -0.34 (0.50), residues: 104 sheet: -0.48 (0.88), residues: 33 loop : -0.70 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 112 HIS 0.003 0.001 HIS A 214 PHE 0.013 0.002 PHE A 350 TYR 0.008 0.001 TYR A 201 ARG 0.004 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.04147 ( 94) hydrogen bonds : angle 4.51690 ( 247) covalent geometry : bond 0.00370 ( 3524) covalent geometry : angle 0.57037 ( 5015) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.260 Fit side-chains REVERT: A 74 GLU cc_start: 0.7045 (mp0) cc_final: 0.6519 (mp0) REVERT: A 111 ARG cc_start: 0.7221 (ptm-80) cc_final: 0.6740 (ptt90) REVERT: A 280 LEU cc_start: 0.6678 (OUTLIER) cc_final: 0.6442 (tp) REVERT: A 302 LYS cc_start: 0.8536 (mtpp) cc_final: 0.8303 (mtpp) outliers start: 9 outliers final: 5 residues processed: 35 average time/residue: 0.2687 time to fit residues: 10.7893 Evaluate side-chains 35 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 326 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 22 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 15 optimal weight: 0.1980 chunk 4 optimal weight: 0.8980 chunk 3 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** 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 = 0.3794 r_free = 0.3794 target = 0.141513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.126185 restraints weight = 4948.031| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.29 r_work: 0.3485 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3524 Z= 0.189 Angle : 0.597 6.563 5015 Z= 0.315 Chirality : 0.040 0.152 571 Planarity : 0.006 0.041 450 Dihedral : 23.303 170.595 1051 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.31 % Allowed : 14.66 % Favored : 81.03 % 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: -0.84 (0.49), residues: 275 helix: -0.22 (0.50), residues: 104 sheet: -0.67 (0.98), residues: 28 loop : -0.69 (0.50), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 112 HIS 0.003 0.002 HIS A 121 PHE 0.015 0.002 PHE A 350 TYR 0.006 0.001 TYR A 201 ARG 0.003 0.001 ARG A 271 Details of bonding type rmsd hydrogen bonds : bond 0.04261 ( 94) hydrogen bonds : angle 4.53204 ( 247) covalent geometry : bond 0.00418 ( 3524) covalent geometry : angle 0.59697 ( 5015) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 30 time to evaluate : 0.289 Fit side-chains REVERT: A 74 GLU cc_start: 0.7111 (mp0) cc_final: 0.6581 (mp0) REVERT: A 111 ARG cc_start: 0.7198 (ptm-80) cc_final: 0.6729 (ptt90) REVERT: A 280 LEU cc_start: 0.6759 (OUTLIER) cc_final: 0.6528 (tp) REVERT: A 302 LYS cc_start: 0.8547 (mtpp) cc_final: 0.8307 (mtpp) outliers start: 10 outliers final: 7 residues processed: 36 average time/residue: 0.2827 time to fit residues: 11.6141 Evaluate side-chains 39 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 105 SER Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 4 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 19 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.9990 chunk 12 optimal weight: 0.0470 chunk 20 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 13 optimal weight: 0.0980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 130 ASN ** 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 = 0.3810 r_free = 0.3810 target = 0.142569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.126774 restraints weight = 4885.670| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.32 r_work: 0.3502 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7103 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3524 Z= 0.144 Angle : 0.555 6.386 5015 Z= 0.293 Chirality : 0.038 0.136 571 Planarity : 0.005 0.040 450 Dihedral : 23.189 171.013 1051 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 4.31 % Allowed : 15.09 % Favored : 80.60 % 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: -0.45 (0.50), residues: 275 helix: 0.19 (0.51), residues: 104 sheet: -0.28 (0.91), residues: 33 loop : -0.59 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 318 HIS 0.002 0.001 HIS A 121 PHE 0.011 0.002 PHE A 350 TYR 0.007 0.001 TYR A 201 ARG 0.002 0.000 ARG A 314 Details of bonding type rmsd hydrogen bonds : bond 0.03988 ( 94) hydrogen bonds : angle 4.34185 ( 247) covalent geometry : bond 0.00319 ( 3524) covalent geometry : angle 0.55533 ( 5015) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.285 Fit side-chains REVERT: A 74 GLU cc_start: 0.7063 (mp0) cc_final: 0.6559 (mp0) REVERT: A 111 ARG cc_start: 0.7180 (ptm-80) cc_final: 0.6695 (ptt90) REVERT: A 280 LEU cc_start: 0.6726 (OUTLIER) cc_final: 0.6489 (tp) REVERT: A 302 LYS cc_start: 0.8465 (mtpp) cc_final: 0.8227 (mtpp) REVERT: A 330 GLU cc_start: 0.7190 (tm-30) cc_final: 0.6964 (tm-30) outliers start: 10 outliers final: 7 residues processed: 39 average time/residue: 0.2649 time to fit residues: 11.9659 Evaluate side-chains 40 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 318 TRP Chi-restraints excluded: chain A residue 326 LEU Chi-restraints excluded: chain A residue 327 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 0.0870 chunk 17 optimal weight: 0.0270 chunk 9 optimal weight: 0.6980 chunk 3 optimal weight: 0.0970 chunk 0 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 0.0000 chunk 14 optimal weight: 1.9990 overall best weight: 0.1818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.145194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.129430 restraints weight = 4815.884| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 1.27 r_work: 0.3530 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3524 Z= 0.121 Angle : 0.542 9.035 5015 Z= 0.290 Chirality : 0.037 0.128 571 Planarity : 0.005 0.040 450 Dihedral : 22.989 171.685 1051 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.02 % Allowed : 16.38 % Favored : 80.60 % 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: -0.10 (0.51), residues: 275 helix: 0.60 (0.52), residues: 104 sheet: -0.02 (0.94), residues: 33 loop : -0.53 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 318 HIS 0.003 0.001 HIS A 121 PHE 0.008 0.001 PHE A 350 TYR 0.006 0.001 TYR A 140 ARG 0.006 0.000 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.03639 ( 94) hydrogen bonds : angle 4.13260 ( 247) covalent geometry : bond 0.00265 ( 3524) covalent geometry : angle 0.54246 ( 5015) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.333 Fit side-chains REVERT: A 74 GLU cc_start: 0.6998 (mp0) cc_final: 0.6563 (mp0) REVERT: A 280 LEU cc_start: 0.6580 (OUTLIER) cc_final: 0.6378 (tp) REVERT: A 302 LYS cc_start: 0.8336 (mtpp) cc_final: 0.8110 (mtpp) outliers start: 7 outliers final: 3 residues processed: 41 average time/residue: 0.2647 time to fit residues: 12.5445 Evaluate side-chains 38 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 299 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 9 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.0020 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 14 optimal weight: 0.0970 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.143886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.127888 restraints weight = 4824.986| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.29 r_work: 0.3511 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3524 Z= 0.137 Angle : 0.571 8.787 5015 Z= 0.299 Chirality : 0.038 0.133 571 Planarity : 0.005 0.040 450 Dihedral : 22.961 172.110 1051 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.02 % Allowed : 17.24 % Favored : 79.74 % 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: -0.07 (0.51), residues: 275 helix: 0.60 (0.52), residues: 104 sheet: -0.15 (1.06), residues: 28 loop : -0.43 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 112 HIS 0.002 0.001 HIS A 214 PHE 0.013 0.002 PHE A 334 TYR 0.007 0.001 TYR A 201 ARG 0.001 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 94) hydrogen bonds : angle 4.21991 ( 247) covalent geometry : bond 0.00303 ( 3524) covalent geometry : angle 0.57096 ( 5015) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 37 time to evaluate : 0.285 Fit side-chains REVERT: A 74 GLU cc_start: 0.7030 (mp0) cc_final: 0.6576 (mp0) REVERT: A 280 LEU cc_start: 0.6654 (OUTLIER) cc_final: 0.6443 (tp) REVERT: A 302 LYS cc_start: 0.8419 (mtpp) cc_final: 0.8174 (mtpp) outliers start: 7 outliers final: 5 residues processed: 43 average time/residue: 0.2393 time to fit residues: 11.9029 Evaluate side-chains 42 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 279 VAL Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 299 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 10 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 30 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 25 optimal weight: 0.0020 chunk 16 optimal weight: 0.3980 overall best weight: 0.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.142784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.127003 restraints weight = 4805.200| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 1.24 r_work: 0.3506 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3524 Z= 0.160 Angle : 0.598 8.560 5015 Z= 0.313 Chirality : 0.039 0.143 571 Planarity : 0.005 0.040 450 Dihedral : 23.019 172.306 1051 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 3.45 % Allowed : 17.24 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.50), residues: 275 helix: 0.52 (0.51), residues: 104 sheet: -0.25 (1.04), residues: 28 loop : -0.48 (0.51), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 112 HIS 0.003 0.001 HIS A 214 PHE 0.013 0.002 PHE A 350 TYR 0.008 0.001 TYR A 201 ARG 0.008 0.001 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 94) hydrogen bonds : angle 4.27536 ( 247) covalent geometry : bond 0.00354 ( 3524) covalent geometry : angle 0.59839 ( 5015) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 550 Ramachandran restraints generated. 275 Oldfield, 0 Emsley, 275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.842 Fit side-chains REVERT: A 74 GLU cc_start: 0.7035 (mp0) cc_final: 0.6568 (mp0) REVERT: A 302 LYS cc_start: 0.8471 (mtpp) cc_final: 0.8217 (mtpp) outliers start: 8 outliers final: 5 residues processed: 42 average time/residue: 0.3992 time to fit residues: 19.4062 Evaluate side-chains 41 residues out of total 234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 299 THR Chi-restraints excluded: chain A residue 347 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 31 random chunks: chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 30 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 0.0170 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 0.0570 chunk 14 optimal weight: 0.0050 chunk 8 optimal weight: 0.3980 chunk 21 optimal weight: 0.7980 overall best weight: 0.1750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.145996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130070 restraints weight = 4856.356| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 1.29 r_work: 0.3538 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3417 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7045 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3524 Z= 0.122 Angle : 0.560 8.530 5015 Z= 0.294 Chirality : 0.037 0.130 571 Planarity : 0.005 0.040 450 Dihedral : 22.906 173.617 1051 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.29 % Allowed : 19.40 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.51), residues: 275 helix: 0.82 (0.53), residues: 104 sheet: 0.07 (0.96), residues: 33 loop : -0.46 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 318 HIS 0.002 0.001 HIS A 214 PHE 0.010 0.001 PHE A 334 TYR 0.007 0.001 TYR A 201 ARG 0.010 0.000 ARG A 134 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 94) hydrogen bonds : angle 4.09777 ( 247) covalent geometry : bond 0.00272 ( 3524) covalent geometry : angle 0.56046 ( 5015) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2802.73 seconds wall clock time: 51 minutes 2.89 seconds (3062.89 seconds total)