Starting phenix.real_space_refine on Wed Mar 5 14:36:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3t_38898/03_2025/8y3t_38898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3t_38898/03_2025/8y3t_38898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8y3t_38898/03_2025/8y3t_38898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3t_38898/03_2025/8y3t_38898.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3t_38898/03_2025/8y3t_38898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3t_38898/03_2025/8y3t_38898.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.004 sd= 0.091 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 6 5.16 5 C 1126 2.51 5 N 308 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 1790 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 895 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 113} Chain breaks: 1 Restraints were copied for chains: B Time building chain proxies: 1.95, per 1000 atoms: 1.09 Number of scatterers: 1790 At special positions: 0 Unit cell: (62.7, 47.5, 60.8, 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 6 16.00 O 350 8.00 N 308 7.00 C 1126 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: 0.54 Conformation dependent library (CDL) restraints added in 264.0 milliseconds 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 448 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 1 sheets defined 21.0% alpha, 35.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 97 through 112 removed outlier: 3.525A pdb=" N LEU A 112 " --> pdb=" O MET A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 124 Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.525A pdb=" N LEU B 112 " --> pdb=" O MET B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 5.457A pdb=" N VAL A 8 " --> pdb=" O VAL A 20 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL A 20 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N GLU A 31 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE A 25 " --> pdb=" O VAL A 29 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL A 29 " --> pdb=" O PHE A 25 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ARG A 83 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ARG B 83 " --> pdb=" O PRO A 93 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N VAL B 29 " --> pdb=" O PHE B 25 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N PHE B 25 " --> pdb=" O VAL B 29 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N GLU B 31 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL B 20 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N VAL B 8 " --> pdb=" O VAL B 20 " (cutoff:3.500A) 94 hydrogen bonds defined for protein. 270 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: 0.47 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 590 1.34 - 1.45: 278 1.45 - 1.57: 942 1.57 - 1.68: 0 1.68 - 1.80: 10 Bond restraints: 1820 Sorted by residual: bond pdb=" CB THR A 45 " pdb=" CG2 THR A 45 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CB THR B 45 " pdb=" CG2 THR B 45 " ideal model delta sigma weight residual 1.521 1.481 0.040 3.30e-02 9.18e+02 1.50e+00 bond pdb=" CB ARG A 56 " pdb=" CG ARG A 56 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.39e+00 bond pdb=" CB ARG B 56 " pdb=" CG ARG B 56 " ideal model delta sigma weight residual 1.520 1.485 0.035 3.00e-02 1.11e+03 1.35e+00 bond pdb=" C VAL B 20 " pdb=" N ALA B 21 " ideal model delta sigma weight residual 1.331 1.313 0.018 1.59e-02 3.96e+03 1.32e+00 ... (remaining 1815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 2260 1.17 - 2.34: 182 2.34 - 3.50: 24 3.50 - 4.67: 6 4.67 - 5.84: 4 Bond angle restraints: 2476 Sorted by residual: angle pdb=" N ASN A 55 " pdb=" CA ASN A 55 " pdb=" C ASN A 55 " ideal model delta sigma weight residual 109.24 112.99 -3.75 1.67e+00 3.59e-01 5.04e+00 angle pdb=" N ASN B 55 " pdb=" CA ASN B 55 " pdb=" C ASN B 55 " ideal model delta sigma weight residual 109.24 112.94 -3.70 1.67e+00 3.59e-01 4.92e+00 angle pdb=" C ALA A 124 " pdb=" N ASN A 125 " pdb=" CA ASN A 125 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.72e+00 angle pdb=" C ALA B 124 " pdb=" N ASN B 125 " pdb=" CA ASN B 125 " ideal model delta sigma weight residual 121.54 125.69 -4.15 1.91e+00 2.74e-01 4.72e+00 angle pdb=" N PRO B 117 " pdb=" CA PRO B 117 " pdb=" C PRO B 117 " ideal model delta sigma weight residual 112.47 116.08 -3.61 2.06e+00 2.36e-01 3.08e+00 ... (remaining 2471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 1016 16.84 - 33.68: 64 33.68 - 50.52: 10 50.52 - 67.36: 2 67.36 - 84.20: 2 Dihedral angle restraints: 1094 sinusoidal: 404 harmonic: 690 Sorted by residual: dihedral pdb=" CA ASN B 55 " pdb=" C ASN B 55 " pdb=" N ARG B 56 " pdb=" CA ARG B 56 " ideal model delta harmonic sigma weight residual 180.00 151.14 28.86 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA ASN A 55 " pdb=" C ASN A 55 " pdb=" N ARG A 56 " pdb=" CA ARG A 56 " ideal model delta harmonic sigma weight residual 180.00 151.16 28.84 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA LYS B 113 " pdb=" C LYS B 113 " pdb=" N ASP B 114 " pdb=" CA ASP B 114 " ideal model delta harmonic sigma weight residual -180.00 -156.91 -23.09 0 5.00e+00 4.00e-02 2.13e+01 ... (remaining 1091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 162 0.034 - 0.069: 82 0.069 - 0.103: 30 0.103 - 0.137: 10 0.137 - 0.171: 6 Chirality restraints: 290 Sorted by residual: chirality pdb=" CA ILE A 128 " pdb=" N ILE A 128 " pdb=" C ILE A 128 " pdb=" CB ILE A 128 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.34e-01 chirality pdb=" CA ILE B 128 " pdb=" N ILE B 128 " pdb=" C ILE B 128 " pdb=" CB ILE B 128 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CB THR A 45 " pdb=" CA THR A 45 " pdb=" OG1 THR A 45 " pdb=" CG2 THR A 45 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 287 not shown) Planarity restraints: 320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 4 " -0.014 2.00e-02 2.50e+03 1.14e-02 2.27e+00 pdb=" CG PHE B 4 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE B 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE B 4 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE B 4 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE B 4 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 4 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 4 " -0.014 2.00e-02 2.50e+03 1.14e-02 2.26e+00 pdb=" CG PHE A 4 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 4 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 4 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 4 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 4 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 4 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN A 116 " 0.024 5.00e-02 4.00e+02 3.58e-02 2.05e+00 pdb=" N PRO A 117 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.020 5.00e-02 4.00e+02 ... (remaining 317 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 280 2.76 - 3.30: 1705 3.30 - 3.83: 3045 3.83 - 4.37: 3731 4.37 - 4.90: 6444 Nonbonded interactions: 15205 Sorted by model distance: nonbonded pdb=" O GLY A 110 " pdb=" ND2 ASN A 116 " model vdw 2.231 3.120 nonbonded pdb=" O GLY B 110 " pdb=" ND2 ASN B 116 " model vdw 2.231 3.120 nonbonded pdb=" NH2 ARG A 56 " pdb=" OD1 ASN B 125 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASN A 125 " pdb=" NH2 ARG B 56 " model vdw 2.380 3.120 nonbonded pdb=" O ALA B 41 " pdb=" NH2 ARG B 83 " model vdw 2.407 3.120 ... (remaining 15200 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' } 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: 0.710 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.540 Find NCS groups from input model: 0.030 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:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 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 : 0.008 0.053 1820 Z= 0.521 Angle : 0.716 5.839 2476 Z= 0.397 Chirality : 0.051 0.171 290 Planarity : 0.004 0.036 320 Dihedral : 12.615 84.198 646 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.54), residues: 230 helix: 0.37 (0.67), residues: 52 sheet: 0.45 (0.58), residues: 78 loop : -0.03 (0.61), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.004 TRP A 32 PHE 0.025 0.003 PHE A 4 TYR 0.008 0.002 TYR A 129 ARG 0.005 0.001 ARG B 38 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.202 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 1.6152 time to fit residues: 80.2138 Evaluate side-chains 43 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 18 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- 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 = 0.3746 r_free = 0.3746 target = 0.149628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129186 restraints weight = 1850.049| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 1.78 r_work: 0.3409 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3274 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7998 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 1820 Z= 0.213 Angle : 0.540 5.493 2476 Z= 0.292 Chirality : 0.046 0.148 290 Planarity : 0.005 0.035 320 Dihedral : 5.271 26.374 252 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.58 % Allowed : 10.31 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.55), residues: 230 helix: 1.38 (0.68), residues: 52 sheet: 0.26 (0.57), residues: 78 loop : 0.31 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 32 PHE 0.015 0.002 PHE B 4 TYR 0.009 0.001 TYR A 42 ARG 0.002 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.193 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 52 average time/residue: 1.5296 time to fit residues: 80.6210 Evaluate side-chains 52 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 7 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 5 optimal weight: 0.0010 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 overall best weight: 2.1994 ------------------------------------------------------------------------------- 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 = 0.3730 r_free = 0.3730 target = 0.148293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127914 restraints weight = 1852.026| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.78 r_work: 0.3393 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 1820 Z= 0.257 Angle : 0.540 5.569 2476 Z= 0.290 Chirality : 0.046 0.147 290 Planarity : 0.005 0.035 320 Dihedral : 5.262 25.992 252 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.12 % Allowed : 11.34 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.55), residues: 230 helix: 1.55 (0.70), residues: 52 sheet: 0.10 (0.56), residues: 78 loop : 0.57 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 32 PHE 0.013 0.002 PHE B 4 TYR 0.008 0.001 TYR A 42 ARG 0.003 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.178 Fit side-chains REVERT: B 103 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8371 (tm) outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 1.6143 time to fit residues: 86.6766 Evaluate side-chains 53 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 1 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 = 0.3768 r_free = 0.3768 target = 0.151115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.130877 restraints weight = 1834.157| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.77 r_work: 0.3457 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3336 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 1820 Z= 0.209 Angle : 0.517 5.469 2476 Z= 0.276 Chirality : 0.045 0.145 290 Planarity : 0.004 0.036 320 Dihedral : 5.022 25.284 252 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.58 % Allowed : 14.95 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.55), residues: 230 helix: 1.73 (0.72), residues: 52 sheet: 0.08 (0.56), residues: 78 loop : 0.70 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 32 PHE 0.010 0.002 PHE B 4 TYR 0.007 0.001 TYR B 58 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.199 Fit side-chains REVERT: B 103 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8315 (tm) outliers start: 5 outliers final: 2 residues processed: 53 average time/residue: 1.5484 time to fit residues: 83.1633 Evaluate side-chains 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3751 r_free = 0.3751 target = 0.149963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.129475 restraints weight = 1839.461| |-----------------------------------------------------------------------------| r_work (start): 0.3541 rms_B_bonded: 1.78 r_work: 0.3435 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3311 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 1820 Z= 0.252 Angle : 0.536 5.538 2476 Z= 0.286 Chirality : 0.046 0.146 290 Planarity : 0.005 0.035 320 Dihedral : 5.166 25.426 252 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 3.09 % Allowed : 17.01 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.56), residues: 230 helix: 1.64 (0.72), residues: 52 sheet: 0.02 (0.56), residues: 78 loop : 0.73 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 32 PHE 0.009 0.002 PHE B 4 TYR 0.008 0.001 TYR B 58 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.189 Fit side-chains REVERT: A 40 GLN cc_start: 0.8430 (OUTLIER) cc_final: 0.8213 (mt0) REVERT: B 89 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7794 (mm-30) REVERT: B 103 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8367 (tm) outliers start: 6 outliers final: 2 residues processed: 53 average time/residue: 1.6448 time to fit residues: 88.3131 Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 89 GLU Chi-restraints excluded: chain B residue 103 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 16 optimal weight: 8.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.8980 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 = 0.3784 r_free = 0.3784 target = 0.153127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132551 restraints weight = 1868.644| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.81 r_work: 0.3484 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3362 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1820 Z= 0.145 Angle : 0.481 5.338 2476 Z= 0.257 Chirality : 0.045 0.142 290 Planarity : 0.004 0.037 320 Dihedral : 4.636 23.096 252 Min Nonbonded Distance : 2.652 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 3.09 % Allowed : 17.01 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.56), residues: 230 helix: 1.94 (0.74), residues: 52 sheet: 0.07 (0.55), residues: 78 loop : 0.83 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 32 PHE 0.008 0.001 PHE A 4 TYR 0.007 0.001 TYR B 42 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.221 Fit side-chains REVERT: A 25 PHE cc_start: 0.8416 (t80) cc_final: 0.8112 (t80) REVERT: A 40 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.8109 (mt0) outliers start: 6 outliers final: 3 residues processed: 55 average time/residue: 1.4985 time to fit residues: 83.5667 Evaluate side-chains 58 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 3 optimal weight: 8.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 19 optimal weight: 0.0970 chunk 15 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 chunk 11 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.7982 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.151601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131001 restraints weight = 1843.631| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 1.80 r_work: 0.3453 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 1820 Z= 0.215 Angle : 0.518 5.476 2476 Z= 0.275 Chirality : 0.045 0.142 290 Planarity : 0.004 0.037 320 Dihedral : 4.931 24.699 252 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 3.09 % Allowed : 18.04 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.56), residues: 230 helix: 1.79 (0.73), residues: 52 sheet: 0.27 (0.54), residues: 88 loop : 0.53 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 32 PHE 0.008 0.001 PHE B 4 TYR 0.008 0.001 TYR B 58 ARG 0.003 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.204 Fit side-chains REVERT: A 40 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.8173 (mt0) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 1.5631 time to fit residues: 83.9134 Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 overall best weight: 3.3586 ------------------------------------------------------------------------------- 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 = 0.3712 r_free = 0.3712 target = 0.147261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.126563 restraints weight = 1884.871| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.82 r_work: 0.3363 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 1820 Z= 0.350 Angle : 0.583 5.699 2476 Z= 0.311 Chirality : 0.047 0.150 290 Planarity : 0.005 0.035 320 Dihedral : 5.458 26.810 252 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.58 % Allowed : 17.53 % Favored : 79.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.55), residues: 230 helix: 1.42 (0.71), residues: 52 sheet: -0.02 (0.55), residues: 78 loop : 0.72 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 32 PHE 0.008 0.002 PHE B 4 TYR 0.009 0.002 TYR B 58 ARG 0.002 0.001 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.195 Fit side-chains REVERT: A 40 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8220 (mt0) outliers start: 5 outliers final: 3 residues processed: 49 average time/residue: 1.5599 time to fit residues: 77.4344 Evaluate side-chains 51 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 47 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.151861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131431 restraints weight = 1868.166| |-----------------------------------------------------------------------------| r_work (start): 0.3579 rms_B_bonded: 1.80 r_work: 0.3477 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 1820 Z= 0.171 Angle : 0.537 9.256 2476 Z= 0.274 Chirality : 0.045 0.144 290 Planarity : 0.004 0.036 320 Dihedral : 4.844 24.134 252 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.06 % Allowed : 19.07 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.55), residues: 230 helix: 1.82 (0.73), residues: 52 sheet: -0.02 (0.54), residues: 78 loop : 0.81 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 32 PHE 0.007 0.001 PHE A 4 TYR 0.008 0.001 TYR B 58 ARG 0.002 0.000 ARG A 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.190 Fit side-chains REVERT: A 25 PHE cc_start: 0.8468 (t80) cc_final: 0.8168 (t80) REVERT: A 40 GLN cc_start: 0.8356 (OUTLIER) cc_final: 0.8141 (mt0) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 1.5131 time to fit residues: 82.7617 Evaluate side-chains 57 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 5 optimal weight: 0.0970 chunk 19 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 20 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 = 0.3756 r_free = 0.3756 target = 0.150748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.129933 restraints weight = 1940.232| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 1.84 r_work: 0.3453 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 1820 Z= 0.199 Angle : 0.547 9.191 2476 Z= 0.279 Chirality : 0.045 0.142 290 Planarity : 0.005 0.038 320 Dihedral : 4.929 24.631 252 Min Nonbonded Distance : 2.664 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Rotamer: Outliers : 2.06 % Allowed : 19.07 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.55), residues: 230 helix: 1.80 (0.73), residues: 52 sheet: -0.00 (0.54), residues: 78 loop : 0.79 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 32 PHE 0.007 0.001 PHE A 4 TYR 0.008 0.001 TYR B 58 ARG 0.003 0.001 ARG A 49 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 460 Ramachandran restraints generated. 230 Oldfield, 0 Emsley, 230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.223 Fit side-chains REVERT: A 40 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.8177 (mt0) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 1.5760 time to fit residues: 84.6508 Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 GLN Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain B residue 45 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 0 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.154601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.134670 restraints weight = 1864.832| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.76 r_work: 0.3500 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 1820 Z= 0.143 Angle : 0.519 8.938 2476 Z= 0.264 Chirality : 0.045 0.141 290 Planarity : 0.005 0.039 320 Dihedral : 4.592 23.043 252 Min Nonbonded Distance : 2.666 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.06 % Allowed : 19.07 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.55), residues: 230 helix: 1.97 (0.74), residues: 52 sheet: 0.17 (0.54), residues: 78 loop : 0.85 (0.64), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 32 PHE 0.007 0.001 PHE A 4 TYR 0.007 0.001 TYR B 58 ARG 0.002 0.000 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2219.78 seconds wall clock time: 38 minutes 48.90 seconds (2328.90 seconds total)