Starting phenix.real_space_refine on Fri Aug 22 12:54:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ot3_17167/08_2025/8ot3_17167.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ot3_17167/08_2025/8ot3_17167.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ot3_17167/08_2025/8ot3_17167.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ot3_17167/08_2025/8ot3_17167.map" model { file = "/net/cci-nas-00/data/ceres_data/8ot3_17167/08_2025/8ot3_17167.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ot3_17167/08_2025/8ot3_17167.cif" } resolution = 2.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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 12 5.16 5 C 1596 2.51 5 N 432 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2460 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 205 Classifications: {'peptide': 28} Link IDs: {'TRANS': 27} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 0.47, per 1000 atoms: 0.19 Number of scatterers: 2460 At special positions: 0 Unit cell: (92.466, 73.786, 42.964, 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 12 16.00 O 420 8.00 N 432 7.00 C 1596 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: 0.17 Conformation dependent library (CDL) restraints added in 90.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 552 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 25.0% 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 'A' and resid 16 through 19 removed outlier: 6.498A pdb=" N LEU A 17 " --> pdb=" O VAL C 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU C 17 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU E 17 " --> pdb=" O VAL G 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU G 17 " --> pdb=" O VAL I 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU I 17 " --> pdb=" O VAL K 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 24 removed outlier: 6.721A pdb=" N ASP C 23 " --> pdb=" O GLU A 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP E 23 " --> pdb=" O GLU C 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP G 23 " --> pdb=" O GLU E 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP I 23 " --> pdb=" O GLU G 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP K 23 " --> pdb=" O GLU I 22 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 16 through 19 removed outlier: 6.498A pdb=" N LEU B 17 " --> pdb=" O VAL D 18 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N LEU D 17 " --> pdb=" O VAL F 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU F 17 " --> pdb=" O VAL H 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU H 17 " --> pdb=" O VAL J 18 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU J 17 " --> pdb=" O VAL L 18 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 24 removed outlier: 6.721A pdb=" N ASP D 23 " --> pdb=" O GLU B 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP F 23 " --> pdb=" O GLU D 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP H 23 " --> pdb=" O GLU F 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP J 23 " --> pdb=" O GLU H 22 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N ASP L 23 " --> pdb=" O GLU J 22 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 30 through 32 30 hydrogen bonds defined for protein. 90 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: 0.31 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: 1.16 - 1.29: 408 1.29 - 1.42: 612 1.42 - 1.55: 1452 1.55 - 1.68: 0 1.68 - 1.80: 24 Bond restraints: 2496 Sorted by residual: bond pdb=" C ILE K 32 " pdb=" O ILE K 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.97e+01 bond pdb=" C ILE G 32 " pdb=" O ILE G 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.97e+01 bond pdb=" C ILE D 32 " pdb=" O ILE D 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.96e+01 bond pdb=" C ILE L 32 " pdb=" O ILE L 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.96e+01 bond pdb=" C ILE J 32 " pdb=" O ILE J 32 " ideal model delta sigma weight residual 1.237 1.161 0.075 1.07e-02 8.73e+03 4.96e+01 ... (remaining 2491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 2101 1.95 - 3.90: 867 3.90 - 5.85: 356 5.85 - 7.80: 0 7.80 - 9.75: 12 Bond angle restraints: 3336 Sorted by residual: angle pdb=" CA GLY I 38 " pdb=" C GLY I 38 " pdb=" O GLY I 38 " ideal model delta sigma weight residual 122.23 118.44 3.79 6.90e-01 2.10e+00 3.02e+01 angle pdb=" CA GLY B 38 " pdb=" C GLY B 38 " pdb=" O GLY B 38 " ideal model delta sigma weight residual 122.23 118.47 3.76 6.90e-01 2.10e+00 2.96e+01 angle pdb=" CA GLY A 38 " pdb=" C GLY A 38 " pdb=" O GLY A 38 " ideal model delta sigma weight residual 122.23 118.48 3.75 6.90e-01 2.10e+00 2.95e+01 angle pdb=" CA GLY L 38 " pdb=" C GLY L 38 " pdb=" O GLY L 38 " ideal model delta sigma weight residual 122.23 118.48 3.75 6.90e-01 2.10e+00 2.95e+01 angle pdb=" CA GLY J 38 " pdb=" C GLY J 38 " pdb=" O GLY J 38 " ideal model delta sigma weight residual 122.23 118.49 3.74 6.90e-01 2.10e+00 2.94e+01 ... (remaining 3331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 1272 16.52 - 33.03: 72 33.03 - 49.55: 36 49.55 - 66.07: 0 66.07 - 82.58: 12 Dihedral angle restraints: 1392 sinusoidal: 516 harmonic: 876 Sorted by residual: dihedral pdb=" CA ILE F 32 " pdb=" CB ILE F 32 " pdb=" CG1 ILE F 32 " pdb=" CD1 ILE F 32 " ideal model delta sinusoidal sigma weight residual 180.00 131.46 48.54 3 1.50e+01 4.44e-03 8.65e+00 dihedral pdb=" CA ILE L 32 " pdb=" CB ILE L 32 " pdb=" CG1 ILE L 32 " pdb=" CD1 ILE L 32 " ideal model delta sinusoidal sigma weight residual 180.00 131.46 48.54 3 1.50e+01 4.44e-03 8.65e+00 dihedral pdb=" CA ILE J 32 " pdb=" CB ILE J 32 " pdb=" CG1 ILE J 32 " pdb=" CD1 ILE J 32 " ideal model delta sinusoidal sigma weight residual 180.00 131.47 48.53 3 1.50e+01 4.44e-03 8.65e+00 ... (remaining 1389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 60 0.045 - 0.091: 72 0.091 - 0.136: 108 0.136 - 0.181: 65 0.181 - 0.227: 79 Chirality restraints: 384 Sorted by residual: chirality pdb=" CA ILE J 31 " pdb=" N ILE J 31 " pdb=" C ILE J 31 " pdb=" CB ILE J 31 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CA ILE A 31 " pdb=" N ILE A 31 " pdb=" C ILE A 31 " pdb=" CB ILE A 31 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA ILE B 31 " pdb=" N ILE B 31 " pdb=" C ILE B 31 " pdb=" CB ILE B 31 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 381 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE I 32 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE I 32 " -0.056 2.00e-02 2.50e+03 pdb=" O ILE I 32 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY I 33 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 32 " 0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C ILE C 32 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE C 32 " 0.021 2.00e-02 2.50e+03 pdb=" N GLY C 33 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 32 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C ILE H 32 " 0.055 2.00e-02 2.50e+03 pdb=" O ILE H 32 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY H 33 " -0.019 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.56 - 3.03: 1370 3.03 - 3.50: 2330 3.50 - 3.96: 3720 3.96 - 4.43: 4345 4.43 - 4.90: 8804 Nonbonded interactions: 20569 Sorted by model distance: nonbonded pdb=" N VAL B 36 " pdb=" O VAL B 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL D 36 " pdb=" O VAL D 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL A 36 " pdb=" O VAL A 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL L 36 " pdb=" O VAL L 36 " model vdw 2.559 2.496 nonbonded pdb=" N VAL I 36 " pdb=" O VAL I 36 " model vdw 2.559 2.496 ... (remaining 20564 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' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.800 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.060 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:5.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7217 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 : 0.014 0.075 2496 Z= 1.104 Angle : 2.331 9.747 3336 Z= 1.679 Chirality : 0.131 0.227 384 Planarity : 0.010 0.032 420 Dihedral : 16.882 82.580 840 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % 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 aren not related in a simple way. whole: -3.27 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.48 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.002 PHE K 20 HIS 0.007 0.002 HIS J 14 Details of bonding type rmsd covalent geometry : bond 0.01419 ( 2496) covalent geometry : angle 2.33059 ( 3336) hydrogen bonds : bond 0.23922 ( 30) hydrogen bonds : angle 11.18109 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.053 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.1792 time to fit residues: 17.5512 Evaluate side-chains 88 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS B 14 HIS C 14 HIS E 14 HIS G 14 HIS I 14 HIS J 14 HIS L 14 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.136228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.119097 restraints weight = 3669.266| |-----------------------------------------------------------------------------| r_work (start): 0.4264 rms_B_bonded: 2.54 r_work: 0.4178 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.4057 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7611 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2496 Z= 0.145 Angle : 0.689 7.009 3336 Z= 0.372 Chirality : 0.052 0.115 384 Planarity : 0.002 0.013 420 Dihedral : 4.094 10.156 324 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.97 % Allowed : 21.83 % Favored : 74.21 % 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 aren not related in a simple way. whole: -3.95 (0.25), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE H 20 HIS 0.015 0.002 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 2496) covalent geometry : angle 0.68947 ( 3336) hydrogen bonds : bond 0.01788 ( 30) hydrogen bonds : angle 3.48994 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.056 Fit side-chains REVERT: A 13 HIS cc_start: 0.6368 (m90) cc_final: 0.6015 (m90) REVERT: C 22 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7570 (tm-30) REVERT: J 22 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7457 (tm-30) REVERT: L 13 HIS cc_start: 0.6842 (m90) cc_final: 0.6461 (m90) REVERT: L 22 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7636 (tm-30) outliers start: 10 outliers final: 5 residues processed: 52 average time/residue: 0.2630 time to fit residues: 14.1955 Evaluate side-chains 45 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS C 14 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.131985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.113794 restraints weight = 3697.464| |-----------------------------------------------------------------------------| r_work (start): 0.4167 rms_B_bonded: 2.63 r_work: 0.4080 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3962 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.4532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.017 2496 Z= 0.161 Angle : 0.649 6.296 3336 Z= 0.345 Chirality : 0.051 0.121 384 Planarity : 0.002 0.010 420 Dihedral : 4.212 10.885 324 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.78 % Allowed : 23.41 % 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 aren not related in a simple way. whole: -4.03 (0.23), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.18), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.003 PHE E 20 HIS 0.011 0.001 HIS C 14 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 2496) covalent geometry : angle 0.64870 ( 3336) hydrogen bonds : bond 0.02332 ( 30) hydrogen bonds : angle 3.88183 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.071 Fit side-chains REVERT: J 22 GLU cc_start: 0.7898 (tm-30) cc_final: 0.7552 (tm-30) REVERT: L 22 GLU cc_start: 0.8033 (tm-30) cc_final: 0.7625 (tm-30) outliers start: 7 outliers final: 7 residues processed: 41 average time/residue: 0.3768 time to fit residues: 15.8933 Evaluate side-chains 43 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 36 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 1 optimal weight: 0.0870 chunk 11 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.133894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.116215 restraints weight = 3660.512| |-----------------------------------------------------------------------------| r_work (start): 0.4220 rms_B_bonded: 2.60 r_work: 0.4137 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4020 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.4020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2496 Z= 0.105 Angle : 0.549 5.380 3336 Z= 0.286 Chirality : 0.051 0.121 384 Planarity : 0.001 0.008 420 Dihedral : 3.953 9.879 324 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.38 % Allowed : 23.81 % 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 aren not related in a simple way. whole: -3.82 (0.23), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.18), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE G 20 HIS 0.002 0.001 HIS K 14 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 2496) covalent geometry : angle 0.54908 ( 3336) hydrogen bonds : bond 0.01577 ( 30) hydrogen bonds : angle 3.42049 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 35 time to evaluate : 0.069 Fit side-chains REVERT: A 35 MET cc_start: 0.7494 (mtt) cc_final: 0.7186 (mtt) REVERT: J 22 GLU cc_start: 0.7835 (tm-30) cc_final: 0.7364 (tm-30) REVERT: K 22 GLU cc_start: 0.7864 (tm-30) cc_final: 0.7509 (tm-30) REVERT: L 22 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7674 (tm-30) outliers start: 6 outliers final: 6 residues processed: 39 average time/residue: 0.4161 time to fit residues: 16.6976 Evaluate side-chains 39 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.133424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.115917 restraints weight = 3646.323| |-----------------------------------------------------------------------------| r_work (start): 0.4212 rms_B_bonded: 2.59 r_work: 0.4126 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.4010 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.4010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 2496 Z= 0.110 Angle : 0.541 4.837 3336 Z= 0.281 Chirality : 0.050 0.122 384 Planarity : 0.001 0.009 420 Dihedral : 3.947 9.291 324 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.78 % Allowed : 23.41 % 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 aren not related in a simple way. whole: -3.57 (0.25), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.19), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE C 20 HIS 0.002 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 2496) covalent geometry : angle 0.54107 ( 3336) hydrogen bonds : bond 0.01702 ( 30) hydrogen bonds : angle 3.49553 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.102 Fit side-chains REVERT: J 22 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7517 (tm-30) REVERT: K 22 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7520 (tm-30) REVERT: L 22 GLU cc_start: 0.8000 (tm-30) cc_final: 0.7585 (tm-30) outliers start: 7 outliers final: 7 residues processed: 37 average time/residue: 0.4483 time to fit residues: 17.0330 Evaluate side-chains 38 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.133483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.115583 restraints weight = 3910.765| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 2.67 r_work: 0.4126 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.4009 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.4009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2496 Z= 0.110 Angle : 0.536 4.478 3336 Z= 0.278 Chirality : 0.050 0.121 384 Planarity : 0.001 0.011 420 Dihedral : 3.976 9.228 324 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 22.62 % Favored : 74.21 % 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 aren not related in a simple way. whole: -3.35 (0.28), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.54 (0.21), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.002 PHE I 20 HIS 0.002 0.000 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 2496) covalent geometry : angle 0.53610 ( 3336) hydrogen bonds : bond 0.01648 ( 30) hydrogen bonds : angle 3.48613 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 27 time to evaluate : 0.071 Fit side-chains REVERT: L 22 GLU cc_start: 0.8009 (tm-30) cc_final: 0.7505 (tm-30) outliers start: 8 outliers final: 7 residues processed: 33 average time/residue: 0.4216 time to fit residues: 14.3578 Evaluate side-chains 34 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 7 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.132988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.114969 restraints weight = 3919.602| |-----------------------------------------------------------------------------| r_work (start): 0.4203 rms_B_bonded: 2.71 r_work: 0.4114 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3995 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.5336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2496 Z= 0.114 Angle : 0.545 4.308 3336 Z= 0.283 Chirality : 0.049 0.120 384 Planarity : 0.002 0.014 420 Dihedral : 3.996 9.694 324 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 22.62 % Favored : 74.21 % 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 aren not related in a simple way. whole: -3.25 (0.30), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.47 (0.23), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE I 20 HIS 0.002 0.000 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 2496) covalent geometry : angle 0.54453 ( 3336) hydrogen bonds : bond 0.01681 ( 30) hydrogen bonds : angle 3.52160 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.095 Fit side-chains REVERT: L 22 GLU cc_start: 0.8032 (tm-30) cc_final: 0.7795 (tm-30) outliers start: 8 outliers final: 7 residues processed: 35 average time/residue: 0.4121 time to fit residues: 14.9171 Evaluate side-chains 36 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 0 optimal weight: 0.6980 chunk 18 optimal weight: 3.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.131446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.113075 restraints weight = 3994.454| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 2.74 r_work: 0.4071 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3951 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.5381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2496 Z= 0.179 Angle : 0.617 4.337 3336 Z= 0.323 Chirality : 0.049 0.120 384 Planarity : 0.002 0.018 420 Dihedral : 4.359 10.559 324 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.97 % Allowed : 21.83 % Favored : 74.21 % 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 aren not related in a simple way. whole: -3.49 (0.29), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.22), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE I 20 HIS 0.004 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 2496) covalent geometry : angle 0.61701 ( 3336) hydrogen bonds : bond 0.02186 ( 30) hydrogen bonds : angle 3.79729 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.125 Fit side-chains REVERT: E 22 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7452 (tm-30) REVERT: L 22 GLU cc_start: 0.8089 (tm-30) cc_final: 0.7733 (tm-30) outliers start: 10 outliers final: 8 residues processed: 41 average time/residue: 0.3565 time to fit residues: 15.1422 Evaluate side-chains 41 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.136885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.119425 restraints weight = 3734.041| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 2.61 r_work: 0.4134 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4011 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2496 Z= 0.110 Angle : 0.578 5.539 3336 Z= 0.300 Chirality : 0.050 0.122 384 Planarity : 0.002 0.022 420 Dihedral : 4.046 9.455 324 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.17 % Allowed : 22.62 % Favored : 74.21 % 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 aren not related in a simple way. whole: -3.31 (0.31), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.001 PHE I 20 HIS 0.002 0.000 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 2496) covalent geometry : angle 0.57802 ( 3336) hydrogen bonds : bond 0.01662 ( 30) hydrogen bonds : angle 3.43288 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 30 time to evaluate : 0.103 Fit side-chains REVERT: A 35 MET cc_start: 0.7488 (mtt) cc_final: 0.7097 (mtt) REVERT: L 22 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7538 (tm-30) outliers start: 8 outliers final: 7 residues processed: 36 average time/residue: 0.3781 time to fit residues: 14.0666 Evaluate side-chains 36 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 12 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 1 optimal weight: 0.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.133090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.115708 restraints weight = 3904.945| |-----------------------------------------------------------------------------| r_work (start): 0.4240 rms_B_bonded: 2.65 r_work: 0.4160 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4049 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.4049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.5511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2496 Z= 0.190 Angle : 0.671 7.537 3336 Z= 0.350 Chirality : 0.049 0.122 384 Planarity : 0.002 0.027 420 Dihedral : 4.383 9.800 324 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.78 % Allowed : 23.41 % 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 aren not related in a simple way. whole: -3.54 (0.30), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.23), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE I 20 HIS 0.004 0.001 HIS E 14 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 2496) covalent geometry : angle 0.67116 ( 3336) hydrogen bonds : bond 0.02174 ( 30) hydrogen bonds : angle 3.81885 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 624 Ramachandran restraints generated. 312 Oldfield, 0 Emsley, 312 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.072 Fit side-chains REVERT: A 35 MET cc_start: 0.7543 (mtt) cc_final: 0.7324 (mtt) REVERT: E 22 GLU cc_start: 0.7987 (tm-30) cc_final: 0.7360 (tm-30) REVERT: L 22 GLU cc_start: 0.8159 (tm-30) cc_final: 0.7696 (tm-30) outliers start: 7 outliers final: 7 residues processed: 41 average time/residue: 0.3890 time to fit residues: 16.4443 Evaluate side-chains 42 residues out of total 252 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 35 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain C residue 26 SER Chi-restraints excluded: chain E residue 26 SER Chi-restraints excluded: chain G residue 26 SER Chi-restraints excluded: chain H residue 26 SER Chi-restraints excluded: chain K residue 26 SER Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 19 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 0.2980 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.136331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.119477 restraints weight = 3783.471| |-----------------------------------------------------------------------------| r_work (start): 0.4233 rms_B_bonded: 2.60 r_work: 0.4134 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.4014 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2496 Z= 0.116 Angle : 0.608 7.736 3336 Z= 0.316 Chirality : 0.050 0.121 384 Planarity : 0.002 0.027 420 Dihedral : 4.026 9.557 324 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.38 % Allowed : 24.21 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.36 (0.32), residues: 312 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.55 (0.24), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE D 20 HIS 0.002 0.000 HIS G 14 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 2496) covalent geometry : angle 0.60755 ( 3336) hydrogen bonds : bond 0.01606 ( 30) hydrogen bonds : angle 3.36060 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1102.53 seconds wall clock time: 19 minutes 26.34 seconds (1166.34 seconds total)