Starting phenix.real_space_refine on Thu Oct 22 17:13:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zkd_74364/10_2026/9zkd_74364.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zkd_74364/10_2026/9zkd_74364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zkd_74364/10_2026/9zkd_74364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zkd_74364/10_2026/9zkd_74364.map" model { file = "/net/cci-nas-00/data/ceres_data/9zkd_74364/10_2026/9zkd_74364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zkd_74364/10_2026/9zkd_74364.cif" } resolution = 2.32 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.007 sd= 0.104 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 1 5.21 5 S 8 5.16 5 C 1071 2.51 5 N 316 2.21 5 O 378 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1778 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1672 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 17, 'TRANS': 190} Chain: "A" Number of atoms: 106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 106 Unusual residues: {' MG': 1, 'ADP': 2} Classifications: {'undetermined': 3, 'water': 51} Link IDs: {None: 53} Time building chain proxies: 0.39, per 1000 atoms: 0.22 Number of scatterers: 1778 At special positions: 0 Unit cell: (61.42, 68.06, 47.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 8 16.00 P 4 15.00 Mg 1 11.99 O 378 8.00 N 316 7.00 C 1071 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.11 Conformation dependent library (CDL) restraints added in 35.2 milliseconds 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 396 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 3 sheets defined 56.2% alpha, 4.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'A' and resid 864 through 869 Processing helix chain 'A' and resid 870 through 889 Processing helix chain 'A' and resid 909 through 913 Processing helix chain 'A' and resid 914 through 935 Processing helix chain 'A' and resid 945 through 950 Processing helix chain 'A' and resid 956 through 960 Processing helix chain 'A' and resid 978 through 1003 Processing helix chain 'A' and resid 1023 through 1027 Processing helix chain 'A' and resid 1028 through 1049 Processing sheet with id=AA1, first strand: chain 'A' and resid 892 through 893 removed outlier: 6.216A pdb=" N THR A 892 " --> pdb=" O HIS A 904 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 938 through 941 Processing sheet with id=AA3, first strand: chain 'A' and resid 1006 through 1007 removed outlier: 6.373A pdb=" N SER A1006 " --> pdb=" O ASN A1018 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 88 hydrogen bonds defined for protein. 243 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.13 Time building geometry restraints manager: 0.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 575 1.34 - 1.46: 308 1.46 - 1.58: 870 1.58 - 1.69: 6 1.69 - 1.81: 12 Bond restraints: 1771 Sorted by residual: bond pdb=" C4 ADP A7601 " pdb=" C5 ADP A7601 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C4 ADP A7602 " pdb=" C5 ADP A7602 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.17e+00 bond pdb=" CG1 ILE A 861 " pdb=" CD1 ILE A 861 " ideal model delta sigma weight residual 1.513 1.488 0.025 3.90e-02 6.57e+02 4.19e-01 bond pdb=" CG LEU A1021 " pdb=" CD2 LEU A1021 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.72e-01 bond pdb=" C GLN A 981 " pdb=" O GLN A 981 " ideal model delta sigma weight residual 1.236 1.229 0.007 1.26e-02 6.30e+03 3.48e-01 ... (remaining 1766 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 2313 1.19 - 2.38: 62 2.38 - 3.57: 27 3.57 - 4.76: 9 4.76 - 5.95: 12 Bond angle restraints: 2423 Sorted by residual: angle pdb=" O1B ADP A7601 " pdb=" PB ADP A7601 " pdb=" O3B ADP A7601 " ideal model delta sigma weight residual 119.90 113.95 5.95 3.00e+00 1.11e-01 3.94e+00 angle pdb=" O1B ADP A7601 " pdb=" PB ADP A7601 " pdb=" O2B ADP A7601 " ideal model delta sigma weight residual 119.90 114.01 5.89 3.00e+00 1.11e-01 3.85e+00 angle pdb=" O1B ADP A7602 " pdb=" PB ADP A7602 " pdb=" O2B ADP A7602 " ideal model delta sigma weight residual 119.90 114.02 5.88 3.00e+00 1.11e-01 3.84e+00 angle pdb=" C1' ADP A7602 " pdb=" C2' ADP A7602 " pdb=" C3' ADP A7602 " ideal model delta sigma weight residual 111.00 105.22 5.78 3.00e+00 1.11e-01 3.72e+00 angle pdb=" O2B ADP A7602 " pdb=" PB ADP A7602 " pdb=" O3B ADP A7602 " ideal model delta sigma weight residual 119.90 114.13 5.77 3.00e+00 1.11e-01 3.70e+00 ... (remaining 2418 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.89: 1038 27.89 - 55.78: 29 55.78 - 83.67: 6 83.67 - 111.55: 1 111.55 - 139.44: 1 Dihedral angle restraints: 1075 sinusoidal: 464 harmonic: 611 Sorted by residual: dihedral pdb=" O2A ADP A7601 " pdb=" O3A ADP A7601 " pdb=" PA ADP A7601 " pdb=" PB ADP A7601 " ideal model delta sinusoidal sigma weight residual 300.00 160.56 139.44 1 2.00e+01 2.50e-03 4.22e+01 dihedral pdb=" O2A ADP A7602 " pdb=" O3A ADP A7602 " pdb=" PA ADP A7602 " pdb=" PB ADP A7602 " ideal model delta sinusoidal sigma weight residual -60.00 0.97 -60.97 1 2.00e+01 2.50e-03 1.24e+01 dihedral pdb=" C5' ADP A7601 " pdb=" O5' ADP A7601 " pdb=" PA ADP A7601 " pdb=" O2A ADP A7601 " ideal model delta sinusoidal sigma weight residual -60.00 0.76 -60.76 1 2.00e+01 2.50e-03 1.23e+01 ... (remaining 1072 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 164 0.031 - 0.062: 69 0.062 - 0.093: 18 0.093 - 0.124: 9 0.124 - 0.154: 4 Chirality restraints: 264 Sorted by residual: chirality pdb=" C3' ADP A7602 " pdb=" C2' ADP A7602 " pdb=" C4' ADP A7602 " pdb=" O3' ADP A7602 " both_signs ideal model delta sigma weight residual False -2.51 -2.66 0.15 2.00e-01 2.50e+01 5.96e-01 chirality pdb=" CA VAL A1022 " pdb=" N VAL A1022 " pdb=" C VAL A1022 " pdb=" CB VAL A1022 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" C1' ADP A7601 " pdb=" C2' ADP A7601 " pdb=" N9 ADP A7601 " pdb=" O4' ADP A7601 " both_signs ideal model delta sigma weight residual False 2.48 2.62 -0.13 2.00e-01 2.50e+01 4.32e-01 ... (remaining 261 not shown) Planarity restraints: 309 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A1022 " -0.018 5.00e-02 4.00e+02 2.73e-02 1.19e+00 pdb=" N PRO A1023 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A1023 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1023 " -0.015 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 955 " -0.014 5.00e-02 4.00e+02 2.16e-02 7.46e-01 pdb=" N PRO A 956 " 0.037 5.00e-02 4.00e+02 pdb=" CA PRO A 956 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 956 " -0.012 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 864 " -0.013 5.00e-02 4.00e+02 2.02e-02 6.50e-01 pdb=" N PRO A 865 " 0.035 5.00e-02 4.00e+02 pdb=" CA PRO A 865 " -0.010 5.00e-02 4.00e+02 pdb=" CD PRO A 865 " -0.011 5.00e-02 4.00e+02 ... (remaining 306 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.32: 5 2.32 - 2.96: 781 2.96 - 3.61: 2680 3.61 - 4.25: 4611 4.25 - 4.90: 7028 Nonbonded interactions: 15105 Sorted by model distance: nonbonded pdb=" O1B ADP A7602 " pdb="MG MG A7603 " model vdw 1.674 2.170 nonbonded pdb=" O1A ADP A7601 " pdb="MG MG A7603 " model vdw 1.688 2.170 nonbonded pdb=" O1B ADP A7601 " pdb="MG MG A7603 " model vdw 1.730 2.170 nonbonded pdb=" O2A ADP A7602 " pdb="MG MG A7603 " model vdw 1.803 2.170 nonbonded pdb=" O1B ADP A7602 " pdb=" O2A ADP A7602 " model vdw 2.319 3.040 ... (remaining 15100 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.020 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.150 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:4.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1771 Z= 0.131 Angle : 0.695 5.951 2423 Z= 0.286 Chirality : 0.042 0.154 264 Planarity : 0.004 0.027 309 Dihedral : 15.043 139.443 679 Min Nonbonded Distance : 1.674 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.75 (0.59), residues: 206 helix: 2.82 (0.50), residues: 103 sheet: -0.59 (1.40), residues: 12 loop : 1.14 (0.67), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1044 TYR 0.007 0.001 TYR A 893 PHE 0.005 0.001 PHE A 851 TRP 0.004 0.001 TRP A 996 HIS 0.006 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 ( 1771) covalent geometry : angle 0.69482 / 0.29 ( 2423) hydrogen bonds : bond 0.11480 / 7.46 ( 88) hydrogen bonds : angle 4.01685 / 2.90 ( 243) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.043 Fit side-chains REVERT: A 868 GLU cc_start: 0.7925 (tp30) cc_final: 0.7646 (tp30) REVERT: A 1016 ARG cc_start: 0.8544 (mtm180) cc_final: 0.8141 (mtp-110) REVERT: A 1033 ARG cc_start: 0.7784 (ttp-110) cc_final: 0.7508 (ttm110) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.5136 time to fit residues: 23.3762 Evaluate side-chains 29 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [12, 13, 1, 8, 16, 15, 9, 11, 18, 6, 4] chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 HIS A1041 GLN A1052 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.139931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.118600 restraints weight = 1741.076| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.27 r_work: 0.3170 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8782 moved from start: 0.1057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1771 Z= 0.143 Angle : 0.731 6.754 2423 Z= 0.300 Chirality : 0.042 0.167 264 Planarity : 0.005 0.031 309 Dihedral : 12.050 141.019 254 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.17 % Allowed : 8.15 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.60), residues: 206 helix: 2.70 (0.50), residues: 105 sheet: -0.88 (1.37), residues: 12 loop : 1.22 (0.72), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 871 TYR 0.009 0.002 TYR A 893 PHE 0.005 0.001 PHE A 851 TRP 0.004 0.001 TRP A 891 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 1771) covalent geometry : angle 0.73100 / 0.30 ( 2423) hydrogen bonds : bond 0.05369 / 3.59 ( 88) hydrogen bonds : angle 3.61880 / 2.67 ( 243) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 29 time to evaluate : 0.065 Fit side-chains REVERT: A 1016 ARG cc_start: 0.8633 (mtm180) cc_final: 0.8231 (mtp-110) REVERT: A 1033 ARG cc_start: 0.7895 (ttp-110) cc_final: 0.7647 (ttm110) outliers start: 4 outliers final: 2 residues processed: 31 average time/residue: 0.8060 time to fit residues: 25.2765 Evaluate side-chains 29 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 938 HIS Chi-restraints excluded: chain A residue 1011 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [14, 8, 6, 12, 2, 11, 3, 0, 5, 19, 10] chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 HIS A1052 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119003 restraints weight = 1747.377| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.28 r_work: 0.3176 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1771 Z= 0.136 Angle : 0.720 6.704 2423 Z= 0.295 Chirality : 0.042 0.161 264 Planarity : 0.004 0.030 309 Dihedral : 11.901 140.732 254 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.63 % Allowed : 11.41 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.60), residues: 206 helix: 2.72 (0.50), residues: 105 sheet: -0.67 (1.49), residues: 12 loop : 1.10 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 871 TYR 0.010 0.002 TYR A 893 PHE 0.005 0.001 PHE A 851 TRP 0.004 0.001 TRP A 891 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.14 ( 1771) covalent geometry : angle 0.72044 / 0.30 ( 2423) hydrogen bonds : bond 0.05115 / 3.43 ( 88) hydrogen bonds : angle 3.48936 / 2.61 ( 243) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.070 Fit side-chains REVERT: A 1016 ARG cc_start: 0.8619 (mtm180) cc_final: 0.8219 (mtp-110) REVERT: A 1033 ARG cc_start: 0.7880 (ttp-110) cc_final: 0.7637 (ttm110) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.7928 time to fit residues: 24.0802 Evaluate side-chains 28 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1011 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [19, 0, 11, 6, 1, 14, 16, 4, 7, 15, 2] chunk 19 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 HIS A1052 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.139617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.118240 restraints weight = 1731.839| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.27 r_work: 0.3167 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8784 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1771 Z= 0.143 Angle : 0.730 6.773 2423 Z= 0.300 Chirality : 0.043 0.168 264 Planarity : 0.004 0.031 309 Dihedral : 12.025 141.709 254 Min Nonbonded Distance : 1.839 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.63 % Allowed : 11.96 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.60), residues: 206 helix: 2.67 (0.50), residues: 105 sheet: -0.93 (1.45), residues: 12 loop : 1.03 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 871 TYR 0.011 0.002 TYR A 893 PHE 0.005 0.001 PHE A 851 TRP 0.004 0.001 TRP A 891 HIS 0.005 0.002 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 1771) covalent geometry : angle 0.72996 / 0.30 ( 2423) hydrogen bonds : bond 0.05235 / 3.51 ( 88) hydrogen bonds : angle 3.50192 / 2.61 ( 243) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.074 Fit side-chains REVERT: A 1016 ARG cc_start: 0.8613 (mtm180) cc_final: 0.8216 (mtp-110) outliers start: 3 outliers final: 1 residues processed: 29 average time/residue: 0.7708 time to fit residues: 22.6393 Evaluate side-chains 30 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1011 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [2, 3, 12, 7, 9, 13, 18, 17, 0, 1, 16] chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 HIS A1052 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.139500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118333 restraints weight = 1704.417| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.25 r_work: 0.3169 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1771 Z= 0.142 Angle : 0.731 6.742 2423 Z= 0.300 Chirality : 0.042 0.168 264 Planarity : 0.004 0.029 309 Dihedral : 12.007 141.481 254 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.17 % Allowed : 10.87 % Favored : 86.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.60), residues: 206 helix: 2.64 (0.50), residues: 105 sheet: -1.00 (1.46), residues: 12 loop : 0.98 (0.69), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 871 TYR 0.012 0.002 TYR A 893 PHE 0.005 0.001 PHE A 851 TRP 0.004 0.001 TRP A 891 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 1771) covalent geometry : angle 0.73064 / 0.30 ( 2423) hydrogen bonds : bond 0.05223 / 3.50 ( 88) hydrogen bonds : angle 3.49281 / 2.61 ( 243) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.073 Fit side-chains REVERT: A 1016 ARG cc_start: 0.8603 (mtm180) cc_final: 0.8208 (mtp-110) REVERT: A 1033 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7626 (ttm110) outliers start: 4 outliers final: 1 residues processed: 32 average time/residue: 0.8931 time to fit residues: 28.9034 Evaluate side-chains 28 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1011 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [0, 7, 16, 1, 3, 12, 13, 4, 15, 18, 9] chunk 0 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 9 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 HIS A1052 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.139607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.118307 restraints weight = 1717.992| |-----------------------------------------------------------------------------| r_work (start): 0.3291 rms_B_bonded: 1.26 r_work: 0.3169 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1771 Z= 0.143 Angle : 0.735 6.729 2423 Z= 0.303 Chirality : 0.043 0.169 264 Planarity : 0.004 0.030 309 Dihedral : 12.015 141.539 254 Min Nonbonded Distance : 1.841 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.17 % Allowed : 11.96 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.59), residues: 206 helix: 2.58 (0.50), residues: 105 sheet: -1.08 (1.43), residues: 12 loop : 0.97 (0.69), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 918 TYR 0.012 0.002 TYR A 893 PHE 0.005 0.001 PHE A 851 TRP 0.004 0.001 TRP A 891 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 1771) covalent geometry : angle 0.73546 / 0.30 ( 2423) hydrogen bonds : bond 0.05218 / 3.50 ( 88) hydrogen bonds : angle 3.48574 / 2.61 ( 243) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 28 time to evaluate : 0.073 Fit side-chains REVERT: A 1016 ARG cc_start: 0.8603 (mtm180) cc_final: 0.8194 (mtp-110) REVERT: A 1033 ARG cc_start: 0.7962 (ttm-80) cc_final: 0.7710 (ttm110) outliers start: 4 outliers final: 1 residues processed: 30 average time/residue: 0.7251 time to fit residues: 22.0780 Evaluate side-chains 29 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1011 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [6, 18, 11, 8, 1, 4, 0, 14, 9, 10, 5] chunk 6 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.140418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.119319 restraints weight = 1699.850| |-----------------------------------------------------------------------------| r_work (start): 0.3304 rms_B_bonded: 1.25 r_work: 0.3183 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 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 0.024 1771 Z= 0.132 Angle : 0.723 6.957 2423 Z= 0.297 Chirality : 0.042 0.162 264 Planarity : 0.004 0.030 309 Dihedral : 11.790 139.723 254 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.09 % Allowed : 13.59 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.49 (0.59), residues: 206 helix: 2.60 (0.50), residues: 105 sheet: -0.96 (1.44), residues: 12 loop : 1.02 (0.69), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 918 TYR 0.012 0.002 TYR A 893 PHE 0.004 0.001 PHE A 851 TRP 0.004 0.001 TRP A1005 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 1771) covalent geometry : angle 0.72314 / 0.30 ( 2423) hydrogen bonds : bond 0.04980 / 3.34 ( 88) hydrogen bonds : angle 3.45727 / 2.59 ( 243) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.073 Fit side-chains REVERT: A 1016 ARG cc_start: 0.8600 (mtm180) cc_final: 0.8201 (mtp-110) REVERT: A 1033 ARG cc_start: 0.7936 (ttm-80) cc_final: 0.7674 (ttm110) outliers start: 2 outliers final: 1 residues processed: 30 average time/residue: 0.8258 time to fit residues: 25.0834 Evaluate side-chains 34 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1011 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [15, 17, 16, 7, 1, 14, 0, 4, 5, 3, 10] chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 0 optimal weight: 0.5980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.141137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120147 restraints weight = 1725.909| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.26 r_work: 0.3193 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1771 Z= 0.125 Angle : 0.716 7.229 2423 Z= 0.294 Chirality : 0.041 0.157 264 Planarity : 0.004 0.029 309 Dihedral : 11.643 138.906 254 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.09 % Allowed : 13.59 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.60), residues: 206 helix: 2.68 (0.50), residues: 105 sheet: -0.90 (1.45), residues: 12 loop : 1.02 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 918 TYR 0.011 0.002 TYR A 893 PHE 0.004 0.001 PHE A 851 TRP 0.004 0.001 TRP A1005 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.13 ( 1771) covalent geometry : angle 0.71621 / 0.29 ( 2423) hydrogen bonds : bond 0.04824 / 3.23 ( 88) hydrogen bonds : angle 3.42231 / 2.57 ( 243) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.080 Fit side-chains REVERT: A 1016 ARG cc_start: 0.8594 (mtm180) cc_final: 0.8200 (mtp-110) REVERT: A 1033 ARG cc_start: 0.7943 (ttm-80) cc_final: 0.7573 (ttm110) outliers start: 2 outliers final: 1 residues processed: 35 average time/residue: 0.8760 time to fit residues: 30.9823 Evaluate side-chains 29 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1011 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [1, 2, 6, 17, 4, 8, 18, 14, 7, 5, 12] chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 8 optimal weight: 0.1980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.0980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.141599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.120598 restraints weight = 1725.578| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 1.25 r_work: 0.3199 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1771 Z= 0.124 Angle : 0.717 7.442 2423 Z= 0.295 Chirality : 0.041 0.154 264 Planarity : 0.004 0.029 309 Dihedral : 11.566 138.422 254 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.63 % Allowed : 13.04 % Favored : 85.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.60), residues: 206 helix: 2.67 (0.50), residues: 105 sheet: -0.84 (1.47), residues: 12 loop : 1.04 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 918 TYR 0.011 0.002 TYR A 893 PHE 0.004 0.001 PHE A 851 TRP 0.004 0.001 TRP A1005 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.12 ( 1771) covalent geometry : angle 0.71730 / 0.30 ( 2423) hydrogen bonds : bond 0.04737 / 3.18 ( 88) hydrogen bonds : angle 3.40557 / 2.56 ( 243) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.049 Fit side-chains REVERT: A 888 GLU cc_start: 0.8381 (mt-10) cc_final: 0.8120 (mm-30) REVERT: A 1016 ARG cc_start: 0.8610 (mtm180) cc_final: 0.8214 (mtp-110) REVERT: A 1033 ARG cc_start: 0.7930 (ttm-80) cc_final: 0.7615 (ttm110) outliers start: 3 outliers final: 1 residues processed: 30 average time/residue: 0.7538 time to fit residues: 22.9116 Evaluate side-chains 29 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1011 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [5, 12, 10, 2, 8, 9, 17, 0, 18, 14, 3] chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.140435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.119369 restraints weight = 1691.150| |-----------------------------------------------------------------------------| r_work (start): 0.3306 rms_B_bonded: 1.24 r_work: 0.3184 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8769 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 1771 Z= 0.137 Angle : 0.732 7.709 2423 Z= 0.304 Chirality : 0.042 0.164 264 Planarity : 0.004 0.028 309 Dihedral : 11.823 140.769 254 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.09 % Allowed : 13.04 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.59), residues: 206 helix: 2.59 (0.50), residues: 105 sheet: -0.98 (1.46), residues: 12 loop : 1.00 (0.69), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 918 TYR 0.012 0.002 TYR A 893 PHE 0.004 0.001 PHE A 851 TRP 0.004 0.001 TRP A 891 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 1771) covalent geometry : angle 0.73226 / 0.30 ( 2423) hydrogen bonds : bond 0.05021 / 3.37 ( 88) hydrogen bonds : angle 3.46274 / 2.60 ( 243) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 412 Ramachandran restraints generated. 206 Oldfield, 0 Emsley, 206 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.068 Fit side-chains REVERT: A 911 HIS cc_start: 0.8204 (m-70) cc_final: 0.7935 (m-70) REVERT: A 1016 ARG cc_start: 0.8614 (mtm180) cc_final: 0.8213 (mtp-110) REVERT: A 1033 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7706 (ttm110) outliers start: 2 outliers final: 1 residues processed: 30 average time/residue: 0.7934 time to fit residues: 24.0995 Evaluate side-chains 30 residues out of total 184 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1011 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: [0, 13, 19, 6, 7, 8, 11, 1, 10, 3, 5] chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 938 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.140080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118883 restraints weight = 1711.957| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 1.26 r_work: 0.3174 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 3.27 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1771 Z= 0.141 Angle : 0.741 8.218 2423 Z= 0.308 Chirality : 0.042 0.166 264 Planarity : 0.004 0.029 309 Dihedral : 11.953 142.372 254 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.09 % Allowed : 13.04 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.59), residues: 206 helix: 2.55 (0.50), residues: 105 sheet: -1.02 (1.43), residues: 12 loop : 1.00 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 918 TYR 0.013 0.002 TYR A 893 PHE 0.005 0.001 PHE A 851 TRP 0.003 0.001 TRP A 891 HIS 0.005 0.001 HIS A 993 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 ( 1771) covalent geometry : angle 0.74091 / 0.31 ( 2423) hydrogen bonds : bond 0.05103 / 3.42 ( 88) hydrogen bonds : angle 3.49715 / 2.63 ( 243) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 996.06 seconds wall clock time: 17 minutes 51.47 seconds (1071.47 seconds total)