Starting phenix.real_space_refine on Tue Aug 4 11:45:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8spa_40677/08_2026/8spa_40677.cif Found real_map, /net/cci-nas-00/data/ceres_data/8spa_40677/08_2026/8spa_40677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8spa_40677/08_2026/8spa_40677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8spa_40677/08_2026/8spa_40677.map" model { file = "/net/cci-nas-00/data/ceres_data/8spa_40677/08_2026/8spa_40677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8spa_40677/08_2026/8spa_40677.cif" } resolution = 3.0 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 ------------------------------------------------------------------------------- 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= 0.002 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: 4 Type Number sf(0) Gaussians S 5 5.16 5 C 1210 2.51 5 N 300 2.21 5 O 355 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-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 1870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 374 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 4, 'TRANS': 44} Restraints were copied for chains: B, C, D, E Time building chain proxies: 0.52, per 1000 atoms: 0.28 Number of scatterers: 1870 At special positions: 0 Unit cell: (63.64, 61.06, 48.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 5 16.00 O 355 8.00 N 300 7.00 C 1210 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: 0.12 Conformation dependent library (CDL) restraints added in 58.0 milliseconds 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 430 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 1 sheets defined 0.0% alpha, 10.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'D' and resid 32 through 37 removed outlier: 6.782A pdb=" N MET A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N GLN C 36 " --> pdb=" O MET A 33 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N PHE A 35 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET C 33 " --> pdb=" O LEU E 34 " (cutoff:3.500A) removed outlier: 8.267A pdb=" N GLN E 36 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N PHE C 35 " --> pdb=" O GLN E 36 " (cutoff:3.500A) 10 hydrogen bonds defined for protein. 30 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: 0.22 Time building geometry restraints manager: 0.16 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: 585 1.34 - 1.46: 441 1.46 - 1.57: 904 1.57 - 1.69: 0 1.69 - 1.80: 10 Bond restraints: 1940 Sorted by residual: bond pdb=" CB VAL A 29 " pdb=" CG1 VAL A 29 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.30e+00 bond pdb=" CB VAL D 29 " pdb=" CG1 VAL D 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL E 29 " pdb=" CG1 VAL E 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.26e+00 bond pdb=" CB VAL B 29 " pdb=" CG1 VAL B 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.25e+00 bond pdb=" CB VAL C 29 " pdb=" CG1 VAL C 29 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.24e+00 ... (remaining 1935 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.10: 2416 1.10 - 2.19: 169 2.19 - 3.29: 54 3.29 - 4.39: 6 4.39 - 5.48: 10 Bond angle restraints: 2655 Sorted by residual: angle pdb=" C PRO D 39 " pdb=" N HIS D 40 " pdb=" CA HIS D 40 " ideal model delta sigma weight residual 122.08 118.87 3.21 1.59e+00 3.96e-01 4.06e+00 angle pdb=" C PRO B 39 " pdb=" N HIS B 40 " pdb=" CA HIS B 40 " ideal model delta sigma weight residual 122.08 118.90 3.18 1.59e+00 3.96e-01 4.01e+00 angle pdb=" C PRO E 39 " pdb=" N HIS E 40 " pdb=" CA HIS E 40 " ideal model delta sigma weight residual 122.08 118.90 3.18 1.59e+00 3.96e-01 4.00e+00 angle pdb=" C PRO A 39 " pdb=" N HIS A 40 " pdb=" CA HIS A 40 " ideal model delta sigma weight residual 122.08 118.94 3.14 1.59e+00 3.96e-01 3.89e+00 angle pdb=" C PRO C 39 " pdb=" N HIS C 40 " pdb=" CA HIS C 40 " ideal model delta sigma weight residual 122.08 118.97 3.11 1.59e+00 3.96e-01 3.83e+00 ... (remaining 2650 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.72: 796 6.72 - 13.44: 129 13.44 - 20.17: 75 20.17 - 26.89: 30 26.89 - 33.61: 20 Dihedral angle restraints: 1050 sinusoidal: 380 harmonic: 670 Sorted by residual: dihedral pdb=" CA HIS A 40 " pdb=" C HIS A 40 " pdb=" N HIS A 41 " pdb=" CA HIS A 41 " ideal model delta harmonic sigma weight residual 180.00 160.78 19.22 0 5.00e+00 4.00e-02 1.48e+01 dihedral pdb=" CA HIS B 40 " pdb=" C HIS B 40 " pdb=" N HIS B 41 " pdb=" CA HIS B 41 " ideal model delta harmonic sigma weight residual 180.00 160.82 19.18 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA HIS D 40 " pdb=" C HIS D 40 " pdb=" N HIS D 41 " pdb=" CA HIS D 41 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 1047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 151 0.030 - 0.060: 94 0.060 - 0.090: 23 0.090 - 0.120: 7 0.120 - 0.150: 10 Chirality restraints: 285 Sorted by residual: chirality pdb=" CA HIS C 40 " pdb=" N HIS C 40 " pdb=" C HIS C 40 " pdb=" CB HIS C 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA HIS B 40 " pdb=" N HIS B 40 " pdb=" C HIS B 40 " pdb=" CB HIS B 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 chirality pdb=" CA HIS E 40 " pdb=" N HIS E 40 " pdb=" C HIS E 40 " pdb=" CB HIS E 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 282 not shown) Planarity restraints: 350 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN E 43 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO E 44 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO E 44 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO E 44 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 43 " 0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO A 44 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 44 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 44 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 43 " 0.022 5.00e-02 4.00e+02 3.38e-02 1.83e+00 pdb=" N PRO B 44 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 44 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 44 " 0.019 5.00e-02 4.00e+02 ... (remaining 347 not shown) Histogram of nonbonded interaction distances: 2.61 - 3.07: 1221 3.07 - 3.53: 1837 3.53 - 3.99: 2653 3.99 - 4.44: 3041 4.44 - 4.90: 5102 Nonbonded interactions: 13854 Sorted by model distance: nonbonded pdb=" O HIS D 40 " pdb=" ND1 HIS D 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS B 40 " pdb=" ND1 HIS B 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS E 40 " pdb=" ND1 HIS E 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS A 40 " pdb=" ND1 HIS A 41 " model vdw 2.614 3.120 nonbonded pdb=" O HIS C 40 " pdb=" ND1 HIS C 41 " model vdw 2.614 3.120 ... (remaining 13849 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.680 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.690 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 1940 Z= 0.239 Angle : 0.753 5.482 2655 Z= 0.403 Chirality : 0.045 0.150 285 Planarity : 0.005 0.034 350 Dihedral : 10.816 33.609 620 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.14 (0.42), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.38 (0.32), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE A 38 TRP 0.001 0.001 TRP D 10 HIS 0.005 0.002 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.24 ( 1940) covalent geometry : angle 0.75278 / 0.40 ( 2655) hydrogen bonds : bond 0.21596 / 15.56 ( 10) hydrogen bonds : angle 7.11050 / 4.79 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.080 Fit side-chains REVERT: C 10 TRP cc_start: 0.7651 (t-100) cc_final: 0.6809 (t-100) REVERT: D 19 GLU cc_start: 0.7977 (tt0) cc_final: 0.7568 (tm-30) REVERT: E 33 MET cc_start: 0.8984 (mtp) cc_final: 0.8663 (mtt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.4338 time to fit residues: 19.5715 Evaluate side-chains 18 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 18 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.095657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.080783 restraints weight = 4619.126| |-----------------------------------------------------------------------------| r_work (start): 0.3880 rms_B_bonded: 3.66 r_work: 0.3764 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.1588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 1940 Z= 0.157 Angle : 0.687 5.117 2655 Z= 0.348 Chirality : 0.043 0.147 285 Planarity : 0.003 0.018 350 Dihedral : 6.325 20.491 240 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 3.33 % Allowed : 12.86 % Favored : 83.81 % 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: -2.77 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.10 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE B 38 TRP 0.007 0.001 TRP E 10 HIS 0.006 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.16 ( 1940) covalent geometry : angle 0.68688 / 0.35 ( 2655) hydrogen bonds : bond 0.03754 / 2.83 ( 10) hydrogen bonds : angle 5.59144 / 3.95 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.078 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7858 (t-100) cc_final: 0.7070 (t-100) REVERT: E 33 MET cc_start: 0.9077 (mtp) cc_final: 0.8862 (mtt) outliers start: 7 outliers final: 4 residues processed: 35 average time/residue: 0.3105 time to fit residues: 11.2298 Evaluate side-chains 24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 20 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain D residue 21 SER Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 18 optimal weight: 0.0770 chunk 19 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 overall best weight: 1.2540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.091824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.076290 restraints weight = 4677.633| |-----------------------------------------------------------------------------| r_work (start): 0.3839 rms_B_bonded: 3.78 r_work: 0.3727 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1940 Z= 0.132 Angle : 0.651 5.620 2655 Z= 0.323 Chirality : 0.041 0.143 285 Planarity : 0.003 0.018 350 Dihedral : 5.985 20.120 240 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.86 % Allowed : 17.62 % Favored : 79.52 % 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: -2.71 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.001 PHE C 35 TRP 0.006 0.001 TRP E 10 HIS 0.005 0.002 HIS A 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.13 ( 1940) covalent geometry : angle 0.65076 / 0.32 ( 2655) hydrogen bonds : bond 0.02623 / 1.97 ( 10) hydrogen bonds : angle 5.13032 / 3.78 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.072 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7948 (t-100) cc_final: 0.6673 (t-100) REVERT: E 10 TRP cc_start: 0.7322 (t-100) cc_final: 0.5516 (p-90) REVERT: E 33 MET cc_start: 0.9152 (mtp) cc_final: 0.8148 (pmt) outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.2475 time to fit residues: 7.7613 Evaluate side-chains 25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 18 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.176504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.145329 restraints weight = 4700.078| |-----------------------------------------------------------------------------| r_work (start): 0.3823 rms_B_bonded: 2.21 r_work: 0.3713 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3635 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 1940 Z= 0.130 Angle : 0.666 7.862 2655 Z= 0.318 Chirality : 0.041 0.140 285 Planarity : 0.003 0.023 350 Dihedral : 5.870 20.434 240 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 2.38 % Allowed : 20.95 % Favored : 76.67 % 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: -2.68 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.04 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.001 PHE C 35 TRP 0.006 0.001 TRP E 10 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.13 ( 1940) covalent geometry : angle 0.66639 / 0.32 ( 2655) hydrogen bonds : bond 0.02302 / 1.75 ( 10) hydrogen bonds : angle 4.59088 / 3.34 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.075 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7961 (t-100) cc_final: 0.6759 (t-100) REVERT: E 10 TRP cc_start: 0.7334 (t-100) cc_final: 0.5428 (p-90) REVERT: E 33 MET cc_start: 0.9154 (mtp) cc_final: 0.8147 (pmt) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.3346 time to fit residues: 9.3398 Evaluate side-chains 23 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 9 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 60.7906 > 50:) chunk 6 optimal weight: 0.0040 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN ** B 36 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 = 0.3991 r_free = 0.3991 target = 0.095116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.079655 restraints weight = 4582.645| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 3.82 r_work: 0.3796 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1940 Z= 0.098 Angle : 0.631 8.664 2655 Z= 0.297 Chirality : 0.040 0.132 285 Planarity : 0.003 0.023 350 Dihedral : 5.532 20.421 240 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.38 % Allowed : 21.90 % Favored : 75.71 % 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: -2.62 (0.45), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE B 38 TRP 0.003 0.000 TRP D 10 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.10 ( 1940) covalent geometry : angle 0.63111 / 0.30 ( 2655) hydrogen bonds : bond 0.01483 / 1.12 ( 10) hydrogen bonds : angle 4.08156 / 3.00 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.076 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7836 (t-100) cc_final: 0.6569 (t-100) REVERT: E 10 TRP cc_start: 0.7319 (t-100) cc_final: 0.5577 (p-90) REVERT: E 33 MET cc_start: 0.8967 (mtp) cc_final: 0.8028 (pmt) outliers start: 5 outliers final: 2 residues processed: 29 average time/residue: 0.1702 time to fit residues: 5.2515 Evaluate side-chains 24 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 18 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.172009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.141477 restraints weight = 4704.167| |-----------------------------------------------------------------------------| r_work (start): 0.3798 rms_B_bonded: 2.14 r_work: 0.3697 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3620 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 1940 Z= 0.179 Angle : 0.670 9.030 2655 Z= 0.332 Chirality : 0.042 0.148 285 Planarity : 0.003 0.023 350 Dihedral : 6.015 19.728 240 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.81 % Allowed : 21.90 % Favored : 74.29 % 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: -2.63 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.00 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE B 50 TRP 0.010 0.001 TRP E 10 HIS 0.005 0.002 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.18 ( 1940) covalent geometry : angle 0.67013 / 0.33 ( 2655) hydrogen bonds : bond 0.02669 / 1.86 ( 10) hydrogen bonds : angle 4.42535 / 3.20 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 22 time to evaluate : 0.067 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.8080 (t-100) cc_final: 0.6886 (t-100) REVERT: E 10 TRP cc_start: 0.7331 (t-100) cc_final: 0.5400 (p-90) REVERT: E 33 MET cc_start: 0.9341 (mtp) cc_final: 0.8218 (pmt) REVERT: E 49 THR cc_start: 0.8448 (p) cc_final: 0.8143 (t) outliers start: 8 outliers final: 5 residues processed: 28 average time/residue: 0.2052 time to fit residues: 6.0378 Evaluate side-chains 25 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 49 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 8.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.174260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4575 r_free = 0.4575 target = 0.142294 restraints weight = 4646.012| |-----------------------------------------------------------------------------| r_work (start): 0.3815 rms_B_bonded: 2.16 r_work: 0.3720 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3647 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.2944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1940 Z= 0.167 Angle : 0.662 9.151 2655 Z= 0.324 Chirality : 0.041 0.145 285 Planarity : 0.003 0.024 350 Dihedral : 6.014 19.690 240 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.81 % Allowed : 22.38 % Favored : 73.81 % 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: -2.74 (0.43), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE B 50 TRP 0.009 0.001 TRP E 10 HIS 0.005 0.002 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 ( 1940) covalent geometry : angle 0.66171 / 0.32 ( 2655) hydrogen bonds : bond 0.02541 / 1.72 ( 10) hydrogen bonds : angle 4.38770 / 3.11 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.8103 (t-100) cc_final: 0.7366 (t-100) REVERT: E 33 MET cc_start: 0.9322 (mtp) cc_final: 0.9044 (mtt) outliers start: 8 outliers final: 7 residues processed: 27 average time/residue: 0.2095 time to fit residues: 5.9476 Evaluate side-chains 26 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 19 time to evaluate : 0.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 21 SER Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 29 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 17 optimal weight: 0.0370 chunk 7 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.178332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.147586 restraints weight = 4685.387| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 2.21 r_work: 0.3814 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3739 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.3170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1940 Z= 0.097 Angle : 0.621 9.791 2655 Z= 0.289 Chirality : 0.039 0.128 285 Planarity : 0.003 0.025 350 Dihedral : 5.477 20.133 240 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.43 % Allowed : 25.24 % Favored : 73.33 % 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: -2.70 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.05 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.001 PHE B 50 TRP 0.004 0.001 TRP D 10 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.10 ( 1940) covalent geometry : angle 0.62052 / 0.29 ( 2655) hydrogen bonds : bond 0.01388 / 1.05 ( 10) hydrogen bonds : angle 4.00052 / 2.90 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.051 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7894 (t-100) cc_final: 0.6592 (t-100) REVERT: E 10 TRP cc_start: 0.7343 (t-100) cc_final: 0.5608 (p-90) REVERT: E 22 PHE cc_start: 0.8450 (m-10) cc_final: 0.7512 (m-10) REVERT: E 33 MET cc_start: 0.8986 (mtp) cc_final: 0.8044 (pmt) REVERT: E 49 THR cc_start: 0.8442 (p) cc_final: 0.8178 (t) outliers start: 3 outliers final: 3 residues processed: 31 average time/residue: 0.1897 time to fit residues: 6.1668 Evaluate side-chains 27 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain D residue 14 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 6 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.0060 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 18 optimal weight: 0.0980 overall best weight: 0.4396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.180420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.150213 restraints weight = 4804.942| |-----------------------------------------------------------------------------| r_work (start): 0.4008 rms_B_bonded: 2.27 r_work: 0.3932 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3860 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1940 Z= 0.092 Angle : 0.628 9.833 2655 Z= 0.286 Chirality : 0.040 0.124 285 Planarity : 0.003 0.024 350 Dihedral : 5.113 19.309 240 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.86 % Allowed : 25.24 % Favored : 71.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.59 (0.45), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.96 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.001 PHE B 50 TRP 0.008 0.001 TRP B 10 HIS 0.004 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.09 ( 1940) covalent geometry : angle 0.62822 / 0.29 ( 2655) hydrogen bonds : bond 0.01229 / 0.82 ( 10) hydrogen bonds : angle 4.03764 / 2.92 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.082 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7797 (t-100) cc_final: 0.6593 (t-100) REVERT: E 10 TRP cc_start: 0.7260 (t-100) cc_final: 0.5629 (p-90) REVERT: E 33 MET cc_start: 0.9015 (mtp) cc_final: 0.7999 (pmt) REVERT: E 49 THR cc_start: 0.8331 (p) cc_final: 0.8067 (t) outliers start: 6 outliers final: 6 residues processed: 38 average time/residue: 0.2375 time to fit residues: 9.4201 Evaluate side-chains 29 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 40 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 3 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN D 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.176006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.146242 restraints weight = 4797.030| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 2.24 r_work: 0.3842 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3770 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1940 Z= 0.136 Angle : 0.692 9.645 2655 Z= 0.316 Chirality : 0.041 0.135 285 Planarity : 0.003 0.022 350 Dihedral : 5.372 18.576 240 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.81 % Allowed : 25.71 % Favored : 70.48 % 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: -2.65 (0.44), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.01 (0.34), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.001 PHE B 50 TRP 0.015 0.002 TRP B 10 HIS 0.005 0.001 HIS C 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.14 ( 1940) covalent geometry : angle 0.69177 / 0.32 ( 2655) hydrogen bonds : bond 0.01900 / 1.27 ( 10) hydrogen bonds : angle 4.00387 / 2.82 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 470 Ramachandran restraints generated. 235 Oldfield, 0 Emsley, 235 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: C 10 TRP cc_start: 0.7906 (t-100) cc_final: 0.6665 (t-100) REVERT: E 10 TRP cc_start: 0.7364 (t-100) cc_final: 0.5527 (p-90) REVERT: E 33 MET cc_start: 0.9175 (mtp) cc_final: 0.8076 (pmt) REVERT: E 49 THR cc_start: 0.8448 (p) cc_final: 0.8173 (t) outliers start: 8 outliers final: 7 residues processed: 33 average time/residue: 0.1290 time to fit residues: 4.5168 Evaluate side-chains 30 residues out of total 210 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain B residue 21 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain C residue 29 VAL Chi-restraints excluded: chain D residue 14 THR Chi-restraints excluded: chain D residue 29 VAL Chi-restraints excluded: chain D residue 40 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 14 optimal weight: 0.1980 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 GLN D 40 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.094014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.078626 restraints weight = 4980.658| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 3.72 r_work: 0.3753 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1940 Z= 0.173 Angle : 0.718 9.592 2655 Z= 0.336 Chirality : 0.042 0.149 285 Planarity : 0.003 0.022 350 Dihedral : 5.715 18.355 240 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 4.76 % Allowed : 25.71 % Favored : 69.52 % 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: -2.87 (0.43), residues: 235 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.33), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE E 22 TRP 0.036 0.003 TRP B 10 HIS 0.007 0.002 HIS D 40 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.17 ( 1940) covalent geometry : angle 0.71758 / 0.34 ( 2655) hydrogen bonds : bond 0.02336 / 1.50 ( 10) hydrogen bonds : angle 4.10370 / 2.88 ( 30) =============================================================================== Job complete usr+sys time: 874.33 seconds wall clock time: 15 minutes 39.65 seconds (939.65 seconds total)