Starting phenix.real_space_refine on Tue Aug 4 11:46:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9onc_70636/08_2026/9onc_70636.cif Found real_map, /net/cci-nas-00/data/ceres_data/9onc_70636/08_2026/9onc_70636.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9onc_70636/08_2026/9onc_70636.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9onc_70636/08_2026/9onc_70636.map" model { file = "/net/cci-nas-00/data/ceres_data/9onc_70636/08_2026/9onc_70636.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9onc_70636/08_2026/9onc_70636.cif" } resolution = 3.64 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= 0.002 sd= 0.009 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 10 5.16 5 C 1160 2.51 5 N 270 2.21 5 O 320 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: 1760 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 176 Classifications: {'peptide': 25} Link IDs: {'TRANS': 24} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'SME:plan-1': 1} Unresolved non-hydrogen planarities: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.69, per 1000 atoms: 0.39 Number of scatterers: 1760 At special positions: 0 Unit cell: (51.045, 79.68, 42.33, 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 10 16.00 O 320 8.00 N 270 7.00 C 1160 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: 0.21 Conformation dependent library (CDL) restraints added in 75.5 milliseconds 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 400 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'H' and resid 31 through 35 removed outlier: 6.966A pdb=" N ILE D 32 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 8.004A pdb=" N SME H 35 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU D 34 " --> pdb=" O SME H 35 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ILE A 32 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N SME D 35 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LEU A 34 " --> pdb=" O SME D 35 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE I 32 " --> pdb=" O ILE E 31 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 39 through 40 removed outlier: 6.379A pdb=" N VAL D 39 " --> pdb=" O VAL H 40 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL A 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 31 through 35 removed outlier: 6.861A pdb=" N ILE B 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 7.911A pdb=" N SME F 35 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N LEU B 34 " --> pdb=" O SME F 35 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N ILE F 32 " --> pdb=" O GLY J 33 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N SME J 35 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N LEU F 34 " --> pdb=" O SME J 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 39 through 40 removed outlier: 6.342A pdb=" N VAL B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL F 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 57 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: 0.43 Time building geometry restraints manager: 0.24 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: 527 1.34 - 1.44: 149 1.44 - 1.55: 1066 1.55 - 1.66: 8 1.66 - 1.76: 20 Bond restraints: 1770 Sorted by residual: bond pdb=" C LEU D 17 " pdb=" N VAL D 18 " ideal model delta sigma weight residual 1.335 1.460 -0.125 1.22e-02 6.72e+03 1.05e+02 bond pdb=" C LEU G 17 " pdb=" N VAL G 18 " ideal model delta sigma weight residual 1.335 1.460 -0.125 1.22e-02 6.72e+03 1.05e+02 bond pdb=" C LEU B 17 " pdb=" N VAL B 18 " ideal model delta sigma weight residual 1.335 1.460 -0.125 1.22e-02 6.72e+03 1.05e+02 bond pdb=" C LEU I 17 " pdb=" N VAL I 18 " ideal model delta sigma weight residual 1.335 1.459 -0.125 1.22e-02 6.72e+03 1.05e+02 bond pdb=" C LEU J 17 " pdb=" N VAL J 18 " ideal model delta sigma weight residual 1.335 1.459 -0.125 1.22e-02 6.72e+03 1.05e+02 ... (remaining 1765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.79: 2260 3.79 - 7.58: 93 7.58 - 11.37: 17 11.37 - 15.16: 0 15.16 - 18.95: 10 Bond angle restraints: 2380 Sorted by residual: angle pdb=" O LEU E 17 " pdb=" C LEU E 17 " pdb=" N VAL E 18 " ideal model delta sigma weight residual 123.00 104.05 18.95 1.60e+00 3.91e-01 1.40e+02 angle pdb=" O LEU I 17 " pdb=" C LEU I 17 " pdb=" N VAL I 18 " ideal model delta sigma weight residual 123.00 104.07 18.93 1.60e+00 3.91e-01 1.40e+02 angle pdb=" O LEU C 17 " pdb=" C LEU C 17 " pdb=" N VAL C 18 " ideal model delta sigma weight residual 123.00 104.07 18.93 1.60e+00 3.91e-01 1.40e+02 angle pdb=" O LEU B 17 " pdb=" C LEU B 17 " pdb=" N VAL B 18 " ideal model delta sigma weight residual 123.00 104.07 18.93 1.60e+00 3.91e-01 1.40e+02 angle pdb=" O LEU F 17 " pdb=" C LEU F 17 " pdb=" N VAL F 18 " ideal model delta sigma weight residual 123.00 104.07 18.93 1.60e+00 3.91e-01 1.40e+02 ... (remaining 2375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 6.88: 700 6.88 - 13.76: 160 13.76 - 20.65: 80 20.65 - 27.53: 40 27.53 - 34.41: 40 Dihedral angle restraints: 1020 sinusoidal: 380 harmonic: 640 Sorted by residual: dihedral pdb=" C ASP J 23 " pdb=" N ASP J 23 " pdb=" CA ASP J 23 " pdb=" CB ASP J 23 " ideal model delta harmonic sigma weight residual -122.60 -130.37 7.77 0 2.50e+00 1.60e-01 9.65e+00 dihedral pdb=" C ASP G 23 " pdb=" N ASP G 23 " pdb=" CA ASP G 23 " pdb=" CB ASP G 23 " ideal model delta harmonic sigma weight residual -122.60 -130.36 7.76 0 2.50e+00 1.60e-01 9.65e+00 dihedral pdb=" C ASP D 23 " pdb=" N ASP D 23 " pdb=" CA ASP D 23 " pdb=" CB ASP D 23 " ideal model delta harmonic sigma weight residual -122.60 -130.33 7.73 0 2.50e+00 1.60e-01 9.57e+00 ... (remaining 1017 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 230 0.072 - 0.144: 60 0.144 - 0.216: 0 0.216 - 0.287: 0 0.287 - 0.359: 10 Chirality restraints: 300 Sorted by residual: chirality pdb=" CA ASP G 23 " pdb=" N ASP G 23 " pdb=" C ASP G 23 " pdb=" CB ASP G 23 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.23e+00 chirality pdb=" CA ASP J 23 " pdb=" N ASP J 23 " pdb=" C ASP J 23 " pdb=" CB ASP J 23 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" CA ASP B 23 " pdb=" N ASP B 23 " pdb=" C ASP B 23 " pdb=" CB ASP B 23 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.18e+00 ... (remaining 297 not shown) Planarity restraints: 290 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU F 17 " 0.108 2.00e-02 2.50e+03 1.97e-01 3.86e+02 pdb=" C LEU F 17 " -0.340 2.00e-02 2.50e+03 pdb=" O LEU F 17 " 0.135 2.00e-02 2.50e+03 pdb=" N VAL F 18 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 17 " 0.108 2.00e-02 2.50e+03 1.96e-01 3.86e+02 pdb=" C LEU B 17 " -0.339 2.00e-02 2.50e+03 pdb=" O LEU B 17 " 0.135 2.00e-02 2.50e+03 pdb=" N VAL B 18 " 0.096 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 17 " 0.108 2.00e-02 2.50e+03 1.96e-01 3.86e+02 pdb=" C LEU D 17 " -0.339 2.00e-02 2.50e+03 pdb=" O LEU D 17 " 0.135 2.00e-02 2.50e+03 pdb=" N VAL D 18 " 0.096 2.00e-02 2.50e+03 ... (remaining 287 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 608 2.85 - 3.36: 1422 3.36 - 3.88: 2670 3.88 - 4.39: 3024 4.39 - 4.90: 4590 Nonbonded interactions: 12314 Sorted by model distance: nonbonded pdb=" O LEU C 17 " pdb=" C VAL C 18 " model vdw 2.340 3.270 nonbonded pdb=" O LEU E 17 " pdb=" C VAL E 18 " model vdw 2.340 3.270 nonbonded pdb=" O LEU A 17 " pdb=" C VAL A 18 " model vdw 2.340 3.270 nonbonded pdb=" O LEU I 17 " pdb=" C VAL I 18 " model vdw 2.340 3.270 nonbonded pdb=" O LEU G 17 " pdb=" C VAL G 18 " model vdw 2.340 3.270 ... (remaining 12309 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' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.060 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.120 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:1.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: -0.0073 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 : 0.013 0.125 1770 Z= 0.880 Angle : 1.953 18.948 2380 Z= 1.190 Chirality : 0.086 0.359 300 Planarity : 0.037 0.197 290 Dihedral : 12.896 34.407 620 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 23.53 % Favored : 76.47 % 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: -1.75 (0.67), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.33 (0.51), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.003 PHE C 19 Details of bonding type rmsd/Z covalent geometry : bond 0.01263 / 0.88 ( 1770) covalent geometry : angle 1.95278 / 1.19 ( 2380) hydrogen bonds : bond 0.30123 / 19.70 ( 19) hydrogen bonds : angle 9.25710 / 5.91 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 19 time to evaluate : 0.072 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 19 average time/residue: 0.0324 time to fit residues: 0.8574 Evaluate side-chains 10 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.065 ------------------------------------------------------------------------------- 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: 6.9990 chunk 13 optimal weight: 9.9990 chunk 1 optimal weight: 0.0030 chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 0.0980 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 overall best weight: 0.9592 ------------------------------------------------------------------------------- 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 = 0.6098 r_free = 0.6098 target = 0.416411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.5674 r_free = 0.5674 target = 0.303264 restraints weight = 1664.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5708 r_free = 0.5708 target = 0.311893 restraints weight = 1302.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5736 r_free = 0.5736 target = 0.318851 restraints weight = 1079.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.5758 r_free = 0.5758 target = 0.324593 restraints weight = 932.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.5786 r_free = 0.5786 target = 0.330179 restraints weight = 829.024| |-----------------------------------------------------------------------------| r_work (final): 0.5735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.0511 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 1770 Z= 0.114 Angle : 0.776 10.449 2380 Z= 0.356 Chirality : 0.053 0.128 300 Planarity : 0.003 0.014 290 Dihedral : 9.776 32.510 310 Min Nonbonded Distance : 2.656 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.00 % Favored : 83.00 % Rotamer: Outliers : 1.76 % Allowed : 26.47 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.25 (0.62), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.71 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.006 0.001 PHE H 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.11 ( 1770) covalent geometry : angle 0.77650 / 0.36 ( 2380) hydrogen bonds : bond 0.03143 / 2.18 ( 19) hydrogen bonds : angle 6.30728 / 3.81 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 11 time to evaluate : 0.065 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 14 average time/residue: 0.0282 time to fit residues: 0.5978 Evaluate side-chains 10 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain J residue 36 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 9.9990 chunk 11 optimal weight: 10.0000 chunk 2 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 1 optimal weight: 20.0000 chunk 14 optimal weight: 0.2980 chunk 19 optimal weight: 0.0770 chunk 8 optimal weight: 9.9990 chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 1.7540 ------------------------------------------------------------------------------- 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 = 0.6236 r_free = 0.6236 target = 0.476532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.6266 r_free = 0.6266 target = 0.439471 restraints weight = 5138.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.6266 r_free = 0.6266 target = 0.441220 restraints weight = 4514.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.6268 r_free = 0.6268 target = 0.442720 restraints weight = 4053.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.6274 r_free = 0.6274 target = 0.443870 restraints weight = 3709.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.6270 r_free = 0.6270 target = 0.444680 restraints weight = 3441.034| |-----------------------------------------------------------------------------| r_work (final): 0.5619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1044 moved from start: 0.5631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1770 Z= 0.156 Angle : 0.744 8.334 2380 Z= 0.367 Chirality : 0.054 0.136 300 Planarity : 0.003 0.015 290 Dihedral : 12.074 45.130 310 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 4.12 % Allowed : 18.24 % Favored : 77.65 % 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: -2.79 (0.55), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.12 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE C 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 ( 1770) covalent geometry : angle 0.74438 / 0.37 ( 2380) hydrogen bonds : bond 0.06055 / 4.09 ( 19) hydrogen bonds : angle 5.38994 / 3.45 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 11 time to evaluate : 0.070 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 16 average time/residue: 0.0259 time to fit residues: 0.6280 Evaluate side-chains 12 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain J residue 36 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 30.0000 chunk 1 optimal weight: 20.0000 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 19 optimal weight: 9.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.0020 chunk 2 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 overall best weight: 4.5794 ------------------------------------------------------------------------------- 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 = 0.5888 r_free = 0.5888 target = 0.416333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.6070 r_free = 0.6070 target = 0.380854 restraints weight = 5314.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.6077 r_free = 0.6077 target = 0.382656 restraints weight = 4471.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.6082 r_free = 0.6082 target = 0.384041 restraints weight = 3885.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.6087 r_free = 0.6087 target = 0.385121 restraints weight = 3465.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.6091 r_free = 0.6091 target = 0.385978 restraints weight = 3156.077| |-----------------------------------------------------------------------------| r_work (final): 0.5342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1488 moved from start: 1.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 1770 Z= 0.230 Angle : 0.988 9.548 2380 Z= 0.506 Chirality : 0.059 0.156 300 Planarity : 0.004 0.012 290 Dihedral : 15.844 58.399 310 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 26.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.50 % Favored : 85.50 % Rotamer: Outliers : 6.47 % Allowed : 20.00 % Favored : 73.53 % 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: -3.25 (0.48), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.003 PHE J 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00496 / 0.23 ( 1770) covalent geometry : angle 0.98805 / 0.51 ( 2380) hydrogen bonds : bond 0.09546 / 6.63 ( 19) hydrogen bonds : angle 7.99671 / 5.70 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 20 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 9 time to evaluate : 0.067 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 20 average time/residue: 0.0211 time to fit residues: 0.6607 Evaluate side-chains 14 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 7 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain F residue 17 LEU Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain I residue 36 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 13 optimal weight: 9.9990 chunk 3 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.0170 chunk 9 optimal weight: 20.0000 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 11 optimal weight: 8.9990 chunk 5 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 overall best weight: 2.2820 ------------------------------------------------------------------------------- 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 = 0.5904 r_free = 0.5904 target = 0.421261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.6065 r_free = 0.6065 target = 0.382385 restraints weight = 5418.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.6065 r_free = 0.6065 target = 0.384238 restraints weight = 4588.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.6068 r_free = 0.6068 target = 0.385561 restraints weight = 4046.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.6068 r_free = 0.6068 target = 0.386596 restraints weight = 3664.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.6073 r_free = 0.6073 target = 0.387376 restraints weight = 3383.988| |-----------------------------------------------------------------------------| r_work (final): 0.5390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1987 moved from start: 1.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1770 Z= 0.124 Angle : 0.746 9.141 2380 Z= 0.360 Chirality : 0.055 0.138 300 Planarity : 0.002 0.012 290 Dihedral : 15.776 59.682 310 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 2.94 % Allowed : 22.94 % Favored : 74.12 % 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: -3.10 (0.49), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE B 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 1770) covalent geometry : angle 0.74603 / 0.36 ( 2380) hydrogen bonds : bond 0.05686 / 3.97 ( 19) hydrogen bonds : angle 6.56313 / 4.32 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 7 time to evaluate : 0.038 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 11 average time/residue: 0.0248 time to fit residues: 0.4405 Evaluate side-chains 11 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain H residue 17 LEU Chi-restraints excluded: chain J residue 32 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 5 optimal weight: 20.0000 chunk 14 optimal weight: 0.5980 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 11 optimal weight: 30.0000 chunk 10 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 27 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5843 r_free = 0.5843 target = 0.409504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.6055 r_free = 0.6055 target = 0.372651 restraints weight = 5416.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.6059 r_free = 0.6059 target = 0.374537 restraints weight = 4555.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.6064 r_free = 0.6064 target = 0.375993 restraints weight = 3962.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.6067 r_free = 0.6067 target = 0.377119 restraints weight = 3532.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.6063 r_free = 0.6063 target = 0.377848 restraints weight = 3218.277| |-----------------------------------------------------------------------------| r_work (final): 0.5383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2062 moved from start: 1.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 1770 Z= 0.149 Angle : 0.773 7.503 2380 Z= 0.382 Chirality : 0.056 0.158 300 Planarity : 0.002 0.009 290 Dihedral : 16.160 58.358 310 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.50 % Favored : 83.50 % Rotamer: Outliers : 4.71 % Allowed : 20.59 % Favored : 74.71 % 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: -3.04 (0.48), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.37), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE G 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 ( 1770) covalent geometry : angle 0.77317 / 0.38 ( 2380) hydrogen bonds : bond 0.06002 / 3.94 ( 19) hydrogen bonds : angle 6.63074 / 4.45 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 6 time to evaluate : 0.062 Fit side-chains REVERT: H 32 ILE cc_start: 0.8840 (pt) cc_final: 0.8556 (mm) outliers start: 8 outliers final: 4 residues processed: 13 average time/residue: 0.0222 time to fit residues: 0.4788 Evaluate side-chains 11 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 7 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain G residue 36 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 9 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 13 optimal weight: 20.0000 chunk 18 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 3 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 overall best weight: 3.2986 ------------------------------------------------------------------------------- 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 = 0.5810 r_free = 0.5810 target = 0.403913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.6074 r_free = 0.6074 target = 0.366884 restraints weight = 5376.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5984 r_free = 0.5984 target = 0.367796 restraints weight = 4354.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5989 r_free = 0.5989 target = 0.368758 restraints weight = 4000.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5988 r_free = 0.5988 target = 0.369363 restraints weight = 3700.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.5990 r_free = 0.5990 target = 0.369920 restraints weight = 3454.585| |-----------------------------------------------------------------------------| r_work (final): 0.5364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2162 moved from start: 1.5008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 1770 Z= 0.154 Angle : 0.797 8.303 2380 Z= 0.396 Chirality : 0.058 0.160 300 Planarity : 0.003 0.009 290 Dihedral : 16.462 59.802 310 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.00 % Favored : 85.00 % Rotamer: Outliers : 3.53 % Allowed : 21.76 % Favored : 74.71 % 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: -3.11 (0.47), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.36), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.003 PHE B 19 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 1770) covalent geometry : angle 0.79740 / 0.40 ( 2380) hydrogen bonds : bond 0.06281 / 4.39 ( 19) hydrogen bonds : angle 6.54447 / 4.52 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 10 time to evaluate : 0.066 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 14 average time/residue: 0.0237 time to fit residues: 0.5335 Evaluate side-chains 13 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 9 time to evaluate : 0.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain F residue 34 LEU Chi-restraints excluded: chain F residue 36 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 15 optimal weight: 20.0000 chunk 11 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 3 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 6.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5727 r_free = 0.5727 target = 0.379146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.5984 r_free = 0.5984 target = 0.343391 restraints weight = 5477.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.5996 r_free = 0.5996 target = 0.345577 restraints weight = 4368.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5993 r_free = 0.5993 target = 0.347175 restraints weight = 3621.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.6010 r_free = 0.6010 target = 0.348470 restraints weight = 3112.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.6015 r_free = 0.6015 target = 0.349529 restraints weight = 2723.931| |-----------------------------------------------------------------------------| r_work (final): 0.5299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2409 moved from start: 1.7546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.088 1770 Z= 0.277 Angle : 1.082 8.677 2380 Z= 0.558 Chirality : 0.065 0.184 300 Planarity : 0.004 0.013 290 Dihedral : 17.811 59.979 310 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 30.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.00 % Favored : 81.00 % Rotamer: Outliers : 5.29 % Allowed : 22.35 % Favored : 72.35 % 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: -3.02 (0.46), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.29 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.004 PHE I 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00592 / 0.28 ( 1770) covalent geometry : angle 1.08228 / 0.56 ( 2380) hydrogen bonds : bond 0.09461 / 6.59 ( 19) hydrogen bonds : angle 7.50016 / 5.25 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 8 time to evaluate : 0.088 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 14 average time/residue: 0.0214 time to fit residues: 0.5166 Evaluate side-chains 9 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 5 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain G residue 36 VAL Chi-restraints excluded: chain I residue 36 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 6 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- 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 = 0.5783 r_free = 0.5783 target = 0.394013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.6009 r_free = 0.6009 target = 0.355326 restraints weight = 5346.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.6018 r_free = 0.6018 target = 0.357541 restraints weight = 4337.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.6014 r_free = 0.6014 target = 0.359196 restraints weight = 3668.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.6029 r_free = 0.6029 target = 0.360472 restraints weight = 3200.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.6025 r_free = 0.6025 target = 0.361428 restraints weight = 2861.120| |-----------------------------------------------------------------------------| r_work (final): 0.5332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2215 moved from start: 1.7507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1770 Z= 0.137 Angle : 0.796 7.956 2380 Z= 0.388 Chirality : 0.057 0.169 300 Planarity : 0.002 0.008 290 Dihedral : 16.617 59.474 310 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 1.76 % Allowed : 25.88 % Favored : 72.35 % 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: -3.10 (0.44), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.34), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE I 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 1770) covalent geometry : angle 0.79623 / 0.39 ( 2380) hydrogen bonds : bond 0.05035 / 3.54 ( 19) hydrogen bonds : angle 7.41454 / 4.96 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.067 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 10 average time/residue: 0.0240 time to fit residues: 0.4292 Evaluate side-chains 11 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 8 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 2 optimal weight: 9.9990 chunk 13 optimal weight: 10.0000 chunk 17 optimal weight: 8.9990 chunk 3 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 16 optimal weight: 8.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5765 r_free = 0.5765 target = 0.383537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.6000 r_free = 0.6000 target = 0.346521 restraints weight = 5406.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.6010 r_free = 0.6010 target = 0.348770 restraints weight = 4331.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.6017 r_free = 0.6017 target = 0.350486 restraints weight = 3599.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.6025 r_free = 0.6025 target = 0.351812 restraints weight = 3080.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.6029 r_free = 0.6029 target = 0.352888 restraints weight = 2703.263| |-----------------------------------------------------------------------------| r_work (final): 0.5352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2418 moved from start: 1.8738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 1770 Z= 0.192 Angle : 0.882 8.470 2380 Z= 0.441 Chirality : 0.059 0.166 300 Planarity : 0.003 0.011 290 Dihedral : 16.928 59.919 310 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 22.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.00 % Favored : 79.00 % Rotamer: Outliers : 1.76 % Allowed : 25.88 % Favored : 72.35 % 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: -2.99 (0.46), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.023 0.003 PHE I 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00409 / 0.19 ( 1770) covalent geometry : angle 0.88193 / 0.44 ( 2380) hydrogen bonds : bond 0.06235 / 4.32 ( 19) hydrogen bonds : angle 7.44155 / 5.13 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 400 Ramachandran restraints generated. 200 Oldfield, 0 Emsley, 200 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.066 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 11 average time/residue: 0.0227 time to fit residues: 0.4072 Evaluate side-chains 12 residues out of total 170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 9 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain E residue 32 ILE Chi-restraints excluded: chain F residue 34 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 20 random chunks: chunk 8 optimal weight: 9.9990 chunk 2 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 0.6980 chunk 12 optimal weight: 0.0020 chunk 16 optimal weight: 0.0050 chunk 14 optimal weight: 8.9990 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 overall best weight: 1.3404 ------------------------------------------------------------------------------- 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 = 0.5823 r_free = 0.5823 target = 0.398825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.6013 r_free = 0.6013 target = 0.359533 restraints weight = 5427.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.6018 r_free = 0.6018 target = 0.361723 restraints weight = 4467.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.6024 r_free = 0.6024 target = 0.363419 restraints weight = 3817.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.6033 r_free = 0.6033 target = 0.364681 restraints weight = 3352.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.6035 r_free = 0.6035 target = 0.365683 restraints weight = 3019.393| |-----------------------------------------------------------------------------| r_work (final): 0.5417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2177 moved from start: 1.8492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 1770 Z= 0.111 Angle : 0.731 7.463 2380 Z= 0.348 Chirality : 0.056 0.163 300 Planarity : 0.002 0.010 290 Dihedral : 16.167 59.724 310 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.00 % Favored : 86.00 % Rotamer: Outliers : 0.59 % Allowed : 27.65 % Favored : 71.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.01 (0.46), residues: 200 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.35), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE I 20 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 1770) covalent geometry : angle 0.73108 / 0.35 ( 2380) hydrogen bonds : bond 0.03644 / 2.59 ( 19) hydrogen bonds : angle 6.88696 / 4.53 ( 57) =============================================================================== Job complete usr+sys time: 632.54 seconds wall clock time: 11 minutes 40.23 seconds (700.23 seconds total)