Starting phenix.real_space_refine on Fri May 9 21:04:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ws8_37801/05_2025/8ws8_37801.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ws8_37801/05_2025/8ws8_37801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ws8_37801/05_2025/8ws8_37801.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ws8_37801/05_2025/8ws8_37801.map" model { file = "/net/cci-nas-00/data/ceres_data/8ws8_37801/05_2025/8ws8_37801.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ws8_37801/05_2025/8ws8_37801.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.014 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 74 5.49 5 S 3 5.16 5 C 2211 2.51 5 N 706 2.21 5 O 898 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 3892 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2348 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2348 Classifications: {'peptide': 298} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 1} Link IDs: {'PTRANS': 29, 'TRANS': 268} 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: 562 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 562 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "B" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 843 Classifications: {'RNA': 40} Modifications used: {'rna2p_pyr': 6, 'rna3p_pur': 16, 'rna3p_pyr': 18} Link IDs: {'rna2p': 6, 'rna3p': 33} 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: 4.10, per 1000 atoms: 1.05 Number of scatterers: 3892 At special positions: 0 Unit cell: (68.64, 89.76, 106.26, 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 74 15.00 O 898 8.00 N 706 7.00 C 2211 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: 1.14 Conformation dependent library (CDL) restraints added in 624.0 milliseconds 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 542 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 1 sheets defined 35.6% alpha, 6.4% beta 13 base pairs and 37 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.885A pdb=" N GLY A 90 " --> pdb=" O GLU A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 99 Processing helix chain 'A' and resid 105 through 117 removed outlier: 3.780A pdb=" N PHE A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA A 114 " --> pdb=" O ASP A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 131 removed outlier: 3.701A pdb=" N LEU A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 169 removed outlier: 3.689A pdb=" N ILE A 144 " --> pdb=" O TYR A 140 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG A 150 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N ASN A 151 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLU A 152 " --> pdb=" O GLU A 148 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N LYS A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 Processing helix chain 'A' and resid 281 through 288 Processing helix chain 'A' and resid 310 through 317 removed outlier: 3.569A pdb=" N TYR A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 332 Processing sheet with id=AA1, first strand: chain 'A' and resid 198 through 199 removed outlier: 3.759A pdb=" N ILE A 347 " --> pdb=" O ASP A 342 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN A 64 " --> pdb=" O ASP A 308 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL A 306 " --> pdb=" O LEU A 66 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE A 296 " --> pdb=" O MET A 307 " (cutoff:3.500A) 75 hydrogen bonds defined for protein. 210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 34 hydrogen bonds 64 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 37 stacking parallelities Total time for adding SS restraints: 1.22 Time building geometry restraints manager: 1.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 516 1.32 - 1.44: 1486 1.44 - 1.57: 1985 1.57 - 1.69: 145 1.69 - 1.81: 4 Bond restraints: 4136 Sorted by residual: bond pdb=" CA LYS A 273 " pdb=" C LYS A 273 " ideal model delta sigma weight residual 1.519 1.560 -0.041 1.16e-02 7.43e+03 1.23e+01 bond pdb=" C THR A 125 " pdb=" O THR A 125 " ideal model delta sigma weight residual 1.235 1.201 0.034 1.20e-02 6.94e+03 8.10e+00 bond pdb=" C ASP A 303 " pdb=" O ASP A 303 " ideal model delta sigma weight residual 1.234 1.205 0.029 1.22e-02 6.72e+03 5.74e+00 bond pdb=" C LYS A 273 " pdb=" N PRO A 274 " ideal model delta sigma weight residual 1.334 1.368 -0.034 1.51e-02 4.39e+03 4.95e+00 bond pdb=" CA LEU A 91 " pdb=" C LEU A 91 " ideal model delta sigma weight residual 1.523 1.498 0.025 1.19e-02 7.06e+03 4.48e+00 ... (remaining 4131 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.89: 5753 1.89 - 3.79: 166 3.79 - 5.68: 17 5.68 - 7.57: 3 7.57 - 9.46: 1 Bond angle restraints: 5940 Sorted by residual: angle pdb=" N ARG A 96 " pdb=" CA ARG A 96 " pdb=" C ARG A 96 " ideal model delta sigma weight residual 111.14 107.23 3.91 1.08e+00 8.57e-01 1.31e+01 angle pdb=" N ILE A 297 " pdb=" CA ILE A 297 " pdb=" C ILE A 297 " ideal model delta sigma weight residual 108.11 113.07 -4.96 1.40e+00 5.10e-01 1.25e+01 angle pdb=" N ASP A 303 " pdb=" CA ASP A 303 " pdb=" C ASP A 303 " ideal model delta sigma weight residual 109.95 104.51 5.44 1.59e+00 3.96e-01 1.17e+01 angle pdb=" N SER A 73 " pdb=" CA SER A 73 " pdb=" C SER A 73 " ideal model delta sigma weight residual 110.80 104.27 6.53 2.13e+00 2.20e-01 9.39e+00 angle pdb=" N ILE A 144 " pdb=" CA ILE A 144 " pdb=" C ILE A 144 " ideal model delta sigma weight residual 110.62 107.54 3.08 1.02e+00 9.61e-01 9.12e+00 ... (remaining 5935 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.92: 2208 34.92 - 69.84: 251 69.84 - 104.76: 16 104.76 - 139.68: 0 139.68 - 174.60: 2 Dihedral angle restraints: 2477 sinusoidal: 1628 harmonic: 849 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 38.61 161.39 1 1.50e+01 4.44e-03 8.31e+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 57.40 174.60 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' A B 18 " pdb=" C1' A B 18 " pdb=" N9 A B 18 " pdb=" C4 A B 18 " ideal model delta sinusoidal sigma weight residual 70.00 3.04 66.96 1 2.00e+01 2.50e-03 1.46e+01 ... (remaining 2474 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 536 0.043 - 0.086: 93 0.086 - 0.129: 38 0.129 - 0.172: 13 0.172 - 0.215: 3 Chirality restraints: 683 Sorted by residual: chirality pdb=" CA ILE A 294 " pdb=" N ILE A 294 " pdb=" C ILE A 294 " pdb=" CB ILE A 294 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CA ASP A 303 " pdb=" N ASP A 303 " pdb=" C ASP A 303 " pdb=" CB ASP A 303 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.17 2.00e-01 2.50e+01 7.62e-01 chirality pdb=" CA ILE A 144 " pdb=" N ILE A 144 " pdb=" C ILE A 144 " pdb=" CB ILE A 144 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.17 2.00e-01 2.50e+01 7.62e-01 ... (remaining 680 not shown) Planarity restraints: 500 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 118 " 0.050 5.00e-02 4.00e+02 7.62e-02 9.29e+00 pdb=" N PRO A 119 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 294 " 0.030 5.00e-02 4.00e+02 4.50e-02 3.23e+00 pdb=" N PRO A 295 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 295 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 295 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP A 75 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.18e+00 pdb=" N PRO A 76 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " 0.025 5.00e-02 4.00e+02 ... (remaining 497 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 884 2.78 - 3.31: 3342 3.31 - 3.84: 7116 3.84 - 4.37: 8363 4.37 - 4.90: 12372 Nonbonded interactions: 32077 Sorted by model distance: nonbonded pdb=" N2 DG C 5 " pdb=" O2 DC D -5 " model vdw 2.253 3.120 nonbonded pdb=" NH1 ARG A 260 " pdb=" O6 G B -16 " model vdw 2.297 3.120 nonbonded pdb=" O2' U B -10 " pdb=" O2 U B -9 " model vdw 2.342 3.040 nonbonded pdb=" NH2 ARG A 260 " pdb=" OP2 U B -17 " model vdw 2.352 3.120 nonbonded pdb=" N1 DG C -12 " pdb=" O6 G B 11 " model vdw 2.357 3.120 ... (remaining 32072 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: 3.560 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.520 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:12.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6403 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 0.041 4136 Z= 0.234 Angle : 0.703 9.464 5940 Z= 0.397 Chirality : 0.044 0.215 683 Planarity : 0.007 0.076 500 Dihedral : 22.749 174.597 1935 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.09 % Favored : 92.91 % Rotamer: Outliers : 0.81 % Allowed : 2.43 % Favored : 96.76 % 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: -0.94 (0.51), residues: 296 helix: -0.09 (0.53), residues: 104 sheet: -1.65 (1.04), residues: 26 loop : -0.74 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 318 HIS 0.001 0.000 HIS A 214 PHE 0.013 0.001 PHE A 137 TYR 0.013 0.002 TYR A 317 ARG 0.007 0.001 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.12271 ( 109) hydrogen bonds : angle 6.22272 ( 274) covalent geometry : bond 0.00410 ( 4136) covalent geometry : angle 0.70318 ( 5940) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 45 time to evaluate : 0.302 Fit side-chains REVERT: A 138 ASN cc_start: 0.7704 (m110) cc_final: 0.7462 (m110) REVERT: A 153 LYS cc_start: 0.6840 (mppt) cc_final: 0.6581 (mptt) REVERT: A 314 ARG cc_start: 0.6120 (ttt-90) cc_final: 0.5339 (ttt-90) outliers start: 2 outliers final: 0 residues processed: 47 average time/residue: 1.5971 time to fit residues: 77.0044 Evaluate side-chains 39 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.4980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.0980 chunk 10 optimal weight: 10.0000 chunk 16 optimal weight: 0.0000 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 HIS ** A 203 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 = 0.4257 r_free = 0.4257 target = 0.183456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.152246 restraints weight = 5195.096| |-----------------------------------------------------------------------------| r_work (start): 0.3861 rms_B_bonded: 1.30 r_work: 0.3759 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6810 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4136 Z= 0.184 Angle : 0.623 12.579 5940 Z= 0.322 Chirality : 0.040 0.147 683 Planarity : 0.006 0.044 500 Dihedral : 25.121 175.360 1341 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.77 % Favored : 92.23 % Rotamer: Outliers : 2.02 % Allowed : 12.55 % Favored : 85.43 % 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: -0.74 (0.51), residues: 296 helix: 0.19 (0.54), residues: 104 sheet: -1.12 (1.09), residues: 26 loop : -0.78 (0.51), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 318 HIS 0.001 0.000 HIS A 214 PHE 0.010 0.002 PHE A 137 TYR 0.008 0.002 TYR A 201 ARG 0.004 0.001 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.05092 ( 109) hydrogen bonds : angle 4.56099 ( 274) covalent geometry : bond 0.00402 ( 4136) covalent geometry : angle 0.62321 ( 5940) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.281 Fit side-chains revert: symmetry clash REVERT: A 97 GLU cc_start: 0.7656 (mp0) cc_final: 0.7426 (mp0) REVERT: A 138 ASN cc_start: 0.7936 (m110) cc_final: 0.7518 (m110) REVERT: A 314 ARG cc_start: 0.6441 (ttt-90) cc_final: 0.5156 (ttt-90) outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 1.8160 time to fit residues: 63.2484 Evaluate side-chains 36 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 336 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 11 optimal weight: 50.0000 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 27 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 5 optimal weight: 0.0980 chunk 4 optimal weight: 0.6980 chunk 14 optimal weight: 0.0670 chunk 10 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 overall best weight: 0.2934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.184298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.153089 restraints weight = 5173.105| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 1.30 r_work: 0.3783 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3657 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6787 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4136 Z= 0.146 Angle : 0.565 10.200 5940 Z= 0.296 Chirality : 0.037 0.143 683 Planarity : 0.005 0.037 500 Dihedral : 24.876 175.557 1341 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.62 % Allowed : 16.60 % Favored : 81.78 % 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: -0.55 (0.52), residues: 296 helix: 0.31 (0.54), residues: 106 sheet: -0.86 (1.15), residues: 26 loop : -0.68 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 318 HIS 0.001 0.001 HIS A 214 PHE 0.009 0.001 PHE A 137 TYR 0.006 0.001 TYR A 201 ARG 0.003 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.04401 ( 109) hydrogen bonds : angle 4.17057 ( 274) covalent geometry : bond 0.00315 ( 4136) covalent geometry : angle 0.56467 ( 5940) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.315 Fit side-chains REVERT: A 97 GLU cc_start: 0.7620 (mp0) cc_final: 0.7377 (mp0) REVERT: A 138 ASN cc_start: 0.7968 (m110) cc_final: 0.7493 (m110) REVERT: A 153 LYS cc_start: 0.7167 (mppt) cc_final: 0.6778 (mptt) REVERT: A 314 ARG cc_start: 0.6386 (ttt-90) cc_final: 0.4964 (ttt-90) outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 1.7355 time to fit residues: 64.0758 Evaluate side-chains 37 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 336 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.0050 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.0670 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.0050 chunk 19 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 overall best weight: 0.2346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** A 203 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 = 0.4275 r_free = 0.4275 target = 0.184871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.153900 restraints weight = 5211.237| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 1.31 r_work: 0.3800 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6756 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4136 Z= 0.134 Angle : 0.549 9.225 5940 Z= 0.289 Chirality : 0.037 0.201 683 Planarity : 0.005 0.035 500 Dihedral : 24.809 175.275 1341 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.83 % Allowed : 17.41 % Favored : 79.76 % 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 (0.52), residues: 296 helix: 0.44 (0.54), residues: 106 sheet: -0.82 (1.15), residues: 26 loop : -0.65 (0.52), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 318 HIS 0.001 0.001 HIS A 135 PHE 0.007 0.001 PHE A 137 TYR 0.006 0.001 TYR A 201 ARG 0.004 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.04190 ( 109) hydrogen bonds : angle 4.01115 ( 274) covalent geometry : bond 0.00288 ( 4136) covalent geometry : angle 0.54866 ( 5940) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.297 Fit side-chains REVERT: A 138 ASN cc_start: 0.7967 (m110) cc_final: 0.7472 (m110) REVERT: A 153 LYS cc_start: 0.7150 (mppt) cc_final: 0.6738 (mptt) REVERT: A 310 ARG cc_start: 0.8076 (mtm180) cc_final: 0.7701 (mtp180) REVERT: A 314 ARG cc_start: 0.6381 (ttt-90) cc_final: 0.4621 (ttt-90) outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 1.5721 time to fit residues: 61.4666 Evaluate side-chains 39 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 34 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 336 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 22 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 0.0070 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN ** A 203 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 = 0.4238 r_free = 0.4238 target = 0.181699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.150349 restraints weight = 5235.347| |-----------------------------------------------------------------------------| r_work (start): 0.3843 rms_B_bonded: 1.30 r_work: 0.3739 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3613 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4136 Z= 0.195 Angle : 0.616 11.464 5940 Z= 0.317 Chirality : 0.039 0.178 683 Planarity : 0.006 0.042 500 Dihedral : 24.962 177.288 1341 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 5.26 % Allowed : 17.00 % Favored : 77.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.51), residues: 296 helix: 0.43 (0.54), residues: 105 sheet: -1.10 (1.12), residues: 26 loop : -0.68 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 318 HIS 0.001 0.001 HIS A 135 PHE 0.013 0.002 PHE A 137 TYR 0.007 0.002 TYR A 265 ARG 0.004 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.05040 ( 109) hydrogen bonds : angle 4.31874 ( 274) covalent geometry : bond 0.00423 ( 4136) covalent geometry : angle 0.61566 ( 5940) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.299 Fit side-chains REVERT: A 153 LYS cc_start: 0.7174 (mppt) cc_final: 0.6765 (mptt) REVERT: A 273 LYS cc_start: 0.5983 (OUTLIER) cc_final: 0.5734 (mtpt) REVERT: A 314 ARG cc_start: 0.6501 (ttt-90) cc_final: 0.4435 (ttt-90) outliers start: 13 outliers final: 6 residues processed: 44 average time/residue: 1.5730 time to fit residues: 70.9979 Evaluate side-chains 42 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 273 LYS Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 336 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.0770 chunk 12 optimal weight: 0.0060 chunk 29 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.2980 chunk 23 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.0970 overall best weight: 0.1050 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 138 ASN ** A 203 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 = 0.4293 r_free = 0.4293 target = 0.186475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.156218 restraints weight = 5248.897| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 1.24 r_work: 0.3831 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3711 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6706 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4136 Z= 0.114 Angle : 0.531 7.422 5940 Z= 0.281 Chirality : 0.036 0.164 683 Planarity : 0.005 0.036 500 Dihedral : 24.585 173.737 1341 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.62 % Allowed : 20.24 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.53), residues: 296 helix: 0.74 (0.56), residues: 100 sheet: -0.77 (1.10), residues: 26 loop : -0.42 (0.53), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 318 HIS 0.001 0.001 HIS A 253 PHE 0.005 0.001 PHE A 334 TYR 0.004 0.001 TYR A 209 ARG 0.003 0.000 ARG A 319 Details of bonding type rmsd hydrogen bonds : bond 0.03730 ( 109) hydrogen bonds : angle 3.91985 ( 274) covalent geometry : bond 0.00241 ( 4136) covalent geometry : angle 0.53135 ( 5940) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.282 Fit side-chains REVERT: A 153 LYS cc_start: 0.7149 (mppt) cc_final: 0.6740 (mptt) REVERT: A 314 ARG cc_start: 0.6328 (ttt-90) cc_final: 0.4406 (ttt-90) outliers start: 4 outliers final: 2 residues processed: 35 average time/residue: 1.4707 time to fit residues: 52.9934 Evaluate side-chains 34 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 0.0670 chunk 10 optimal weight: 5.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 127 GLN A 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.181333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.150574 restraints weight = 5177.712| |-----------------------------------------------------------------------------| r_work (start): 0.3842 rms_B_bonded: 1.23 r_work: 0.3737 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6855 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4136 Z= 0.213 Angle : 0.637 11.795 5940 Z= 0.325 Chirality : 0.040 0.167 683 Planarity : 0.006 0.044 500 Dihedral : 24.867 178.417 1341 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.24 % Allowed : 19.43 % Favored : 77.33 % 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: -0.38 (0.52), residues: 296 helix: 0.56 (0.55), residues: 105 sheet: -1.07 (1.11), residues: 26 loop : -0.59 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 249 HIS 0.001 0.001 HIS A 135 PHE 0.014 0.002 PHE A 137 TYR 0.008 0.002 TYR A 201 ARG 0.003 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.05174 ( 109) hydrogen bonds : angle 4.30278 ( 274) covalent geometry : bond 0.00465 ( 4136) covalent geometry : angle 0.63653 ( 5940) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 35 time to evaluate : 0.325 Fit side-chains REVERT: A 153 LYS cc_start: 0.7194 (mppt) cc_final: 0.6766 (mptt) REVERT: A 314 ARG cc_start: 0.6511 (ttt-90) cc_final: 0.4534 (ttt-90) outliers start: 8 outliers final: 6 residues processed: 39 average time/residue: 1.6264 time to fit residues: 65.1139 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 336 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 0.0980 chunk 23 optimal weight: 0.0070 chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 0.0870 chunk 28 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.2776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 138 ASN ** A 203 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 = 0.4261 r_free = 0.4261 target = 0.183531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.152356 restraints weight = 5162.608| |-----------------------------------------------------------------------------| r_work (start): 0.3866 rms_B_bonded: 1.32 r_work: 0.3760 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.1755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4136 Z= 0.140 Angle : 0.567 9.167 5940 Z= 0.296 Chirality : 0.037 0.194 683 Planarity : 0.005 0.035 500 Dihedral : 24.711 176.347 1341 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.43 % Allowed : 20.24 % Favored : 77.33 % 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: -0.32 (0.52), residues: 296 helix: 0.59 (0.54), residues: 105 sheet: -1.07 (1.08), residues: 26 loop : -0.53 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 318 HIS 0.001 0.001 HIS A 135 PHE 0.008 0.001 PHE A 137 TYR 0.006 0.001 TYR A 201 ARG 0.003 0.000 ARG A 262 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 109) hydrogen bonds : angle 4.11119 ( 274) covalent geometry : bond 0.00297 ( 4136) covalent geometry : angle 0.56723 ( 5940) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.307 Fit side-chains REVERT: A 153 LYS cc_start: 0.7190 (mppt) cc_final: 0.6770 (mptt) REVERT: A 314 ARG cc_start: 0.6457 (ttt-90) cc_final: 0.4491 (ttt-90) outliers start: 6 outliers final: 5 residues processed: 35 average time/residue: 1.5358 time to fit residues: 55.3252 Evaluate side-chains 37 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 336 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 19 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 0.0020 chunk 9 optimal weight: 1.9990 overall best weight: 0.5728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 138 ASN ** A 203 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 = 0.4234 r_free = 0.4234 target = 0.180740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3838 r_free = 0.3838 target = 0.148841 restraints weight = 5168.673| |-----------------------------------------------------------------------------| r_work (start): 0.3834 rms_B_bonded: 1.32 r_work: 0.3728 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6873 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4136 Z= 0.208 Angle : 0.638 11.314 5940 Z= 0.326 Chirality : 0.040 0.170 683 Planarity : 0.006 0.045 500 Dihedral : 24.832 179.256 1341 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.24 % Allowed : 19.43 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.51), residues: 296 helix: 0.43 (0.54), residues: 105 sheet: -1.33 (1.07), residues: 26 loop : -0.61 (0.51), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 249 HIS 0.001 0.001 HIS A 135 PHE 0.013 0.002 PHE A 137 TYR 0.008 0.002 TYR A 265 ARG 0.004 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.05317 ( 109) hydrogen bonds : angle 4.44157 ( 274) covalent geometry : bond 0.00449 ( 4136) covalent geometry : angle 0.63844 ( 5940) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 36 time to evaluate : 0.288 Fit side-chains REVERT: A 97 GLU cc_start: 0.7649 (mm-30) cc_final: 0.7404 (mp0) REVERT: A 153 LYS cc_start: 0.7197 (mppt) cc_final: 0.6771 (mptt) REVERT: A 314 ARG cc_start: 0.6516 (ttt-90) cc_final: 0.4351 (ttt-90) outliers start: 8 outliers final: 6 residues processed: 41 average time/residue: 1.5511 time to fit residues: 65.3227 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 336 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 13 optimal weight: 0.2980 chunk 21 optimal weight: 0.0970 chunk 12 optimal weight: 0.5980 chunk 10 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 138 ASN ** A 203 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 = 0.4243 r_free = 0.4243 target = 0.181261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.149565 restraints weight = 5246.658| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.30 r_work: 0.3750 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4136 Z= 0.173 Angle : 0.597 10.421 5940 Z= 0.307 Chirality : 0.039 0.177 683 Planarity : 0.006 0.044 500 Dihedral : 24.708 178.313 1341 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 2.83 % Allowed : 20.24 % Favored : 76.92 % 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: -0.47 (0.51), residues: 296 helix: 0.41 (0.54), residues: 105 sheet: -1.31 (1.08), residues: 26 loop : -0.56 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 249 HIS 0.002 0.001 HIS A 253 PHE 0.011 0.001 PHE A 137 TYR 0.008 0.002 TYR A 87 ARG 0.004 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.04611 ( 109) hydrogen bonds : angle 4.28146 ( 274) covalent geometry : bond 0.00376 ( 4136) covalent geometry : angle 0.59745 ( 5940) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 592 Ramachandran restraints generated. 296 Oldfield, 0 Emsley, 296 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.274 Fit side-chains REVERT: A 153 LYS cc_start: 0.7133 (mppt) cc_final: 0.6736 (mptt) REVERT: A 314 ARG cc_start: 0.6480 (ttt-90) cc_final: 0.4470 (ttt-90) outliers start: 7 outliers final: 7 residues processed: 38 average time/residue: 1.4915 time to fit residues: 58.3627 Evaluate side-chains 41 residues out of total 249 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 VAL Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 264 TRP Chi-restraints excluded: chain A residue 302 LYS Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 336 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 0 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.0670 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 28 optimal weight: 0.2980 chunk 3 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 127 GLN A 138 ASN ** A 203 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 = 0.4246 r_free = 0.4246 target = 0.181550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.149990 restraints weight = 5177.959| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.25 r_work: 0.3752 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6831 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4136 Z= 0.147 Angle : 0.580 10.218 5940 Z= 0.300 Chirality : 0.038 0.186 683 Planarity : 0.005 0.044 500 Dihedral : 24.697 178.387 1341 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.24 % Allowed : 19.84 % Favored : 76.92 % 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: -0.43 (0.51), residues: 296 helix: 0.45 (0.54), residues: 105 sheet: -1.31 (1.08), residues: 26 loop : -0.53 (0.52), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 318 HIS 0.001 0.001 HIS A 135 PHE 0.011 0.001 PHE A 137 TYR 0.006 0.001 TYR A 265 ARG 0.002 0.000 ARG A 115 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 109) hydrogen bonds : angle 4.25609 ( 274) covalent geometry : bond 0.00316 ( 4136) covalent geometry : angle 0.58011 ( 5940) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3608.43 seconds wall clock time: 62 minutes 55.86 seconds (3775.86 seconds total)