Starting phenix.real_space_refine on Tue Feb 3 12:18:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kl3_62399/02_2026/9kl3_62399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kl3_62399/02_2026/9kl3_62399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9kl3_62399/02_2026/9kl3_62399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kl3_62399/02_2026/9kl3_62399.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9kl3_62399/02_2026/9kl3_62399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kl3_62399/02_2026/9kl3_62399.map" } resolution = 3.24 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= 0.034 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 1 5.16 5 C 637 2.51 5 N 183 2.21 5 O 205 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-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1026 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1011 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 7, 'TRANS': 129} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'A2G': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.30, per 1000 atoms: 0.29 Number of scatterers: 1026 At special positions: 0 Unit cell: (47.141, 54.162, 49.147, 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 1 16.00 O 205 8.00 N 183 7.00 C 637 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: 0.08 Conformation dependent library (CDL) restraints added in 26.5 milliseconds 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 238 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 3 sheets defined 2.2% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 59 removed outlier: 15.777A pdb=" N TYR A 8 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 11.068A pdb=" N LEU A 21 " --> pdb=" O TYR A 8 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N ILE A 10 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU A 17 " --> pdb=" O ASN A 12 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR A 30 " --> pdb=" O GLY A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 55 through 59 Processing sheet with id=AA3, first strand: chain 'A' and resid 88 through 91 removed outlier: 3.532A pdb=" N LEU A 104 " --> pdb=" O ALA A 101 " (cutoff:3.500A) 32 hydrogen bonds defined for protein. 81 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: 0.07 Time building geometry restraints manager: 0.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 172 1.31 - 1.43: 264 1.43 - 1.56: 609 1.56 - 1.68: 0 1.68 - 1.80: 2 Bond restraints: 1047 Sorted by residual: bond pdb=" C7 A2G A 201 " pdb=" N2 A2G A 201 " ideal model delta sigma weight residual 1.349 1.450 -0.101 2.00e-02 2.50e+03 2.54e+01 bond pdb=" C1 A2G A 201 " pdb=" O5 A2G A 201 " ideal model delta sigma weight residual 1.385 1.466 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" C5 A2G A 201 " pdb=" O5 A2G A 201 " ideal model delta sigma weight residual 1.419 1.491 -0.072 2.00e-02 2.50e+03 1.31e+01 bond pdb=" C3 A2G A 201 " pdb=" O3 A2G A 201 " ideal model delta sigma weight residual 1.403 1.464 -0.061 2.00e-02 2.50e+03 9.30e+00 bond pdb=" C3 A2G A 201 " pdb=" C4 A2G A 201 " ideal model delta sigma weight residual 1.530 1.476 0.054 2.00e-02 2.50e+03 7.28e+00 ... (remaining 1042 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.05: 1386 1.05 - 2.10: 30 2.10 - 3.15: 10 3.15 - 4.20: 7 4.20 - 5.25: 3 Bond angle restraints: 1436 Sorted by residual: angle pdb=" C4 A2G A 201 " pdb=" C5 A2G A 201 " pdb=" C6 A2G A 201 " ideal model delta sigma weight residual 113.93 108.68 5.25 3.00e+00 1.11e-01 3.07e+00 angle pdb=" C8 A2G A 201 " pdb=" C7 A2G A 201 " pdb=" N2 A2G A 201 " ideal model delta sigma weight residual 115.31 120.03 -4.72 3.00e+00 1.11e-01 2.48e+00 angle pdb=" C4 A2G A 201 " pdb=" C3 A2G A 201 " pdb=" O3 A2G A 201 " ideal model delta sigma weight residual 113.03 108.55 4.48 3.00e+00 1.11e-01 2.23e+00 angle pdb=" C PRO A 94 " pdb=" N GLY A 95 " pdb=" CA GLY A 95 " ideal model delta sigma weight residual 123.44 121.69 1.75 1.19e+00 7.06e-01 2.16e+00 angle pdb=" C3 A2G A 201 " pdb=" C4 A2G A 201 " pdb=" C5 A2G A 201 " ideal model delta sigma weight residual 108.51 112.44 -3.93 3.00e+00 1.11e-01 1.71e+00 ... (remaining 1431 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.51: 544 11.51 - 23.02: 52 23.02 - 34.52: 14 34.52 - 46.03: 5 46.03 - 57.53: 2 Dihedral angle restraints: 617 sinusoidal: 240 harmonic: 377 Sorted by residual: dihedral pdb=" CB ARG A 44 " pdb=" CG ARG A 44 " pdb=" CD ARG A 44 " pdb=" NE ARG A 44 " ideal model delta sinusoidal sigma weight residual -180.00 -132.22 -47.78 3 1.50e+01 4.44e-03 8.54e+00 dihedral pdb=" N ASN A 63 " pdb=" CA ASN A 63 " pdb=" CB ASN A 63 " pdb=" CG ASN A 63 " ideal model delta sinusoidal sigma weight residual -60.00 -96.88 36.88 3 1.50e+01 4.44e-03 6.41e+00 dihedral pdb=" N ASN A 41 " pdb=" CA ASN A 41 " pdb=" CB ASN A 41 " pdb=" CG ASN A 41 " ideal model delta sinusoidal sigma weight residual -60.00 -96.26 36.26 3 1.50e+01 4.44e-03 6.27e+00 ... (remaining 614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 101 0.025 - 0.050: 32 0.050 - 0.075: 17 0.075 - 0.099: 9 0.099 - 0.124: 11 Chirality restraints: 170 Sorted by residual: chirality pdb=" CA ILE A 46 " pdb=" N ILE A 46 " pdb=" C ILE A 46 " pdb=" CB ILE A 46 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.86e-01 chirality pdb=" CA VAL A 47 " pdb=" N VAL A 47 " pdb=" C VAL A 47 " pdb=" CB VAL A 47 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA ILE A 3 " pdb=" N ILE A 3 " pdb=" C ILE A 3 " pdb=" CB ILE A 3 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.74e-01 ... (remaining 167 not shown) Planarity restraints: 187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 72 " 0.023 5.00e-02 4.00e+02 3.43e-02 1.88e+00 pdb=" N PRO A 73 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 73 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 73 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 3 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 4 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 4 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 4 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 93 " 0.016 5.00e-02 4.00e+02 2.40e-02 9.19e-01 pdb=" N PRO A 94 " -0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 94 " 0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 94 " 0.013 5.00e-02 4.00e+02 ... (remaining 184 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 302 2.83 - 3.35: 803 3.35 - 3.86: 1546 3.86 - 4.38: 1792 4.38 - 4.90: 3383 Nonbonded interactions: 7826 Sorted by model distance: nonbonded pdb=" OG1 THR A 88 " pdb=" OG SER A 100 " model vdw 2.312 3.040 nonbonded pdb=" OD1 ASP A 20 " pdb=" ND2 ASN A 42 " model vdw 2.334 3.120 nonbonded pdb=" OD1 ASN A 109 " pdb=" OG1 THR A 120 " model vdw 2.384 3.040 nonbonded pdb=" NH2 ARG A 22 " pdb=" O GLY A 116 " model vdw 2.453 3.120 nonbonded pdb=" O ILE A 3 " pdb=" NE ARG A 55 " model vdw 2.459 3.120 ... (remaining 7821 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.910 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: 0.010 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 2.090 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.101 1047 Z= 0.307 Angle : 0.547 5.252 1436 Z= 0.257 Chirality : 0.044 0.124 170 Planarity : 0.004 0.034 187 Dihedral : 10.961 57.534 379 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.70), residues: 135 helix: None (None), residues: 0 sheet: 0.92 (0.91), residues: 32 loop : -1.49 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 11 TYR 0.003 0.001 TYR A 8 PHE 0.005 0.001 PHE A 134 TRP 0.004 0.001 TRP A 35 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00616 ( 1047) covalent geometry : angle 0.54741 ( 1436) hydrogen bonds : bond 0.06494 ( 24) hydrogen bonds : angle 5.09633 ( 81) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 0.0194 time to fit residues: 0.1902 Evaluate side-chains 6 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 6 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.124471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.101063 restraints weight = 1118.838| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.16 r_work: 0.3042 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.0711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1047 Z= 0.133 Angle : 0.494 4.560 1436 Z= 0.250 Chirality : 0.045 0.134 170 Planarity : 0.005 0.037 187 Dihedral : 5.652 36.585 170 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % 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: -1.23 (0.71), residues: 135 helix: None (None), residues: 0 sheet: 1.01 (0.96), residues: 31 loop : -1.54 (0.59), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 86 TYR 0.003 0.001 TYR A 8 PHE 0.007 0.002 PHE A 134 TRP 0.002 0.001 TRP A 35 HIS 0.002 0.001 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 1047) covalent geometry : angle 0.49369 ( 1436) hydrogen bonds : bond 0.03970 ( 24) hydrogen bonds : angle 4.36199 ( 81) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.021 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0143 time to fit residues: 0.1862 Evaluate side-chains 6 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 3 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 = 0.3338 r_free = 0.3338 target = 0.121814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.098408 restraints weight = 1155.735| |-----------------------------------------------------------------------------| r_work (start): 0.3141 rms_B_bonded: 2.18 r_work: 0.2999 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 moved from start: 0.1084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 1047 Z= 0.161 Angle : 0.528 4.954 1436 Z= 0.268 Chirality : 0.046 0.136 170 Planarity : 0.005 0.040 187 Dihedral : 4.891 17.848 170 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.89 % Allowed : 6.60 % Favored : 91.51 % 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: -1.25 (0.71), residues: 135 helix: None (None), residues: 0 sheet: 0.99 (0.97), residues: 31 loop : -1.55 (0.59), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 55 TYR 0.005 0.002 TYR A 8 PHE 0.007 0.002 PHE A 67 TRP 0.003 0.001 TRP A 35 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 1047) covalent geometry : angle 0.52821 ( 1436) hydrogen bonds : bond 0.04106 ( 24) hydrogen bonds : angle 4.41113 ( 81) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 4 time to evaluate : 0.021 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 6 average time/residue: 0.0160 time to fit residues: 0.1467 Evaluate side-chains 6 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 4 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 88 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 2.9990 chunk 11 optimal weight: 0.0770 chunk 9 optimal weight: 0.0050 chunk 2 optimal weight: 0.4980 chunk 6 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 0 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.4152 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.125974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.102617 restraints weight = 1141.813| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.16 r_work: 0.3056 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2901 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1047 Z= 0.083 Angle : 0.417 3.204 1436 Z= 0.217 Chirality : 0.043 0.135 170 Planarity : 0.005 0.036 187 Dihedral : 4.015 13.310 170 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.94 % Allowed : 10.38 % Favored : 88.68 % 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: -1.20 (0.71), residues: 135 helix: None (None), residues: 0 sheet: 0.93 (0.93), residues: 32 loop : -1.51 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 55 TYR 0.003 0.001 TYR A 8 PHE 0.006 0.001 PHE A 134 TRP 0.003 0.000 TRP A 35 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 1047) covalent geometry : angle 0.41653 ( 1436) hydrogen bonds : bond 0.03216 ( 24) hydrogen bonds : angle 3.97072 ( 81) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.022 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 7 average time/residue: 0.0215 time to fit residues: 0.2230 Evaluate side-chains 7 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 12 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3386 r_free = 0.3386 target = 0.125603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.102159 restraints weight = 1118.850| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.16 r_work: 0.3056 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.0997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1047 Z= 0.099 Angle : 0.438 3.804 1436 Z= 0.225 Chirality : 0.044 0.132 170 Planarity : 0.005 0.037 187 Dihedral : 4.048 13.666 170 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.94 % Allowed : 11.32 % Favored : 87.74 % 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: -1.17 (0.71), residues: 135 helix: None (None), residues: 0 sheet: 0.95 (0.93), residues: 32 loop : -1.48 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 22 TYR 0.004 0.001 TYR A 8 PHE 0.006 0.002 PHE A 134 TRP 0.003 0.001 TRP A 35 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 1047) covalent geometry : angle 0.43767 ( 1436) hydrogen bonds : bond 0.03365 ( 24) hydrogen bonds : angle 3.97908 ( 81) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.041 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 7 average time/residue: 0.0258 time to fit residues: 0.2641 Evaluate side-chains 7 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3348 r_free = 0.3348 target = 0.122601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.099037 restraints weight = 1175.301| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 2.19 r_work: 0.3024 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 1047 Z= 0.150 Angle : 0.509 5.118 1436 Z= 0.256 Chirality : 0.046 0.133 170 Planarity : 0.005 0.039 187 Dihedral : 4.566 14.874 170 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.83 % Allowed : 9.43 % Favored : 87.74 % 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: -1.25 (0.71), residues: 135 helix: None (None), residues: 0 sheet: 0.91 (0.97), residues: 31 loop : -1.52 (0.60), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 22 TYR 0.005 0.001 TYR A 18 PHE 0.007 0.002 PHE A 67 TRP 0.003 0.001 TRP A 35 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 1047) covalent geometry : angle 0.50890 ( 1436) hydrogen bonds : bond 0.03910 ( 24) hydrogen bonds : angle 4.27237 ( 81) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 4 time to evaluate : 0.022 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 7 average time/residue: 0.0159 time to fit residues: 0.1668 Evaluate side-chains 7 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 4 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 100 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 12 optimal weight: 1.9990 chunk 2 optimal weight: 0.0870 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.124824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.101743 restraints weight = 1140.715| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 2.12 r_work: 0.3061 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1047 Z= 0.107 Angle : 0.449 3.817 1436 Z= 0.230 Chirality : 0.044 0.132 170 Planarity : 0.005 0.036 187 Dihedral : 4.231 14.230 170 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.89 % Allowed : 11.32 % Favored : 86.79 % 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: -1.24 (0.71), residues: 135 helix: None (None), residues: 0 sheet: 0.88 (0.93), residues: 32 loop : -1.52 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 55 TYR 0.004 0.001 TYR A 8 PHE 0.006 0.002 PHE A 134 TRP 0.004 0.001 TRP A 35 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 1047) covalent geometry : angle 0.44888 ( 1436) hydrogen bonds : bond 0.03450 ( 24) hydrogen bonds : angle 4.06161 ( 81) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.041 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 8 average time/residue: 0.0261 time to fit residues: 0.3045 Evaluate side-chains 8 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 88 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 7 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 0 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.124237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.100666 restraints weight = 1146.404| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.18 r_work: 0.3077 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 1047 Z= 0.120 Angle : 0.466 4.228 1436 Z= 0.237 Chirality : 0.044 0.131 170 Planarity : 0.005 0.037 187 Dihedral : 4.294 14.449 170 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.89 % Allowed : 11.32 % Favored : 86.79 % 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: -1.24 (0.71), residues: 135 helix: None (None), residues: 0 sheet: 0.90 (0.94), residues: 32 loop : -1.54 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 55 TYR 0.004 0.001 TYR A 8 PHE 0.007 0.002 PHE A 134 TRP 0.003 0.001 TRP A 35 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 1047) covalent geometry : angle 0.46604 ( 1436) hydrogen bonds : bond 0.03597 ( 24) hydrogen bonds : angle 4.10365 ( 81) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.044 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 8 average time/residue: 0.0279 time to fit residues: 0.3245 Evaluate side-chains 8 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 6 time to evaluate : 0.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 88 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 0.1980 chunk 6 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.3415 r_free = 0.3415 target = 0.126999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.104146 restraints weight = 1155.909| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.09 r_work: 0.3035 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.1089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 1047 Z= 0.099 Angle : 0.436 3.592 1436 Z= 0.224 Chirality : 0.044 0.132 170 Planarity : 0.005 0.035 187 Dihedral : 4.074 13.923 170 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.83 % Allowed : 10.38 % Favored : 86.79 % 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: -1.20 (0.71), residues: 135 helix: None (None), residues: 0 sheet: 0.93 (0.94), residues: 32 loop : -1.51 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 55 TYR 0.004 0.001 TYR A 8 PHE 0.007 0.002 PHE A 134 TRP 0.004 0.001 TRP A 35 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 1047) covalent geometry : angle 0.43561 ( 1436) hydrogen bonds : bond 0.03346 ( 24) hydrogen bonds : angle 3.96237 ( 81) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.043 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 10 average time/residue: 0.0287 time to fit residues: 0.3902 Evaluate side-chains 10 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 7 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 3 optimal weight: 4.9990 chunk 7 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3378 r_free = 0.3378 target = 0.125174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.101213 restraints weight = 1129.748| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.21 r_work: 0.3023 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.1099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 1047 Z= 0.106 Angle : 0.446 3.855 1436 Z= 0.228 Chirality : 0.044 0.131 170 Planarity : 0.005 0.036 187 Dihedral : 4.116 14.053 170 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.83 % Allowed : 10.38 % Favored : 86.79 % 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: -1.21 (0.72), residues: 135 helix: None (None), residues: 0 sheet: 0.92 (0.94), residues: 32 loop : -1.51 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 55 TYR 0.004 0.001 TYR A 8 PHE 0.006 0.002 PHE A 134 TRP 0.003 0.001 TRP A 35 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 1047) covalent geometry : angle 0.44636 ( 1436) hydrogen bonds : bond 0.03445 ( 24) hydrogen bonds : angle 4.00347 ( 81) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 270 Ramachandran restraints generated. 135 Oldfield, 0 Emsley, 135 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.021 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 9 average time/residue: 0.0153 time to fit residues: 0.1976 Evaluate side-chains 9 residues out of total 106 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 6 time to evaluate : 0.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 100 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 13 random chunks: chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 10.0000 chunk 9 optimal weight: 0.0270 chunk 11 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.6840 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.125100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.101137 restraints weight = 1134.495| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.22 r_work: 0.3060 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 1047 Z= 0.107 Angle : 0.447 3.852 1436 Z= 0.228 Chirality : 0.044 0.131 170 Planarity : 0.005 0.036 187 Dihedral : 4.122 14.063 170 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 0.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.83 % Allowed : 10.38 % Favored : 86.79 % 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: -1.21 (0.71), residues: 135 helix: None (None), residues: 0 sheet: 0.92 (0.94), residues: 32 loop : -1.51 (0.60), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 55 TYR 0.004 0.001 TYR A 8 PHE 0.006 0.002 PHE A 134 TRP 0.003 0.001 TRP A 35 HIS 0.001 0.000 HIS A 80 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 1047) covalent geometry : angle 0.44682 ( 1436) hydrogen bonds : bond 0.03447 ( 24) hydrogen bonds : angle 4.00904 ( 81) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 468.09 seconds wall clock time: 8 minutes 42.98 seconds (522.98 seconds total)