Starting phenix.real_space_refine on Mon Jan 13 13:08:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y3t_38898/01_2025/8y3t_38898.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y3t_38898/01_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_38898/01_2025/8y3t_38898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y3t_38898/01_2025/8y3t_38898.map" model { file = "/net/cci-nas-00/data/ceres_data/8y3t_38898/01_2025/8y3t_38898.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y3t_38898/01_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-5571/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: 1.92, per 1000 atoms: 1.07 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: 0.44 Conformation dependent library (CDL) restraints added in 231.6 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: 0.44 Time building geometry restraints manager: 0.52 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: 0.700 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.190 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:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.970 ------------------------------------------------------------------------------- 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 : 0.213 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 1.5992 time to fit residues: 79.4116 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 : 0.245 ------------------------------------------------------------------------------- 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 = 43)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129194 restraints weight = 1850.049| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.78 r_work: 0.3410 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 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 : 0.220 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 52 average time/residue: 1.7212 time to fit residues: 90.7839 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 : 0.193 ------------------------------------------------------------------------------- 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: 1.9990 chunk 1 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 0.0570 chunk 15 optimal weight: 8.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 overall best weight: 2.2106 ------------------------------------------------------------------------------- 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 = 0.3729 r_free = 0.3729 target = 0.148305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127978 restraints weight = 1852.163| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 1.77 r_work: 0.3389 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 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= 0.259 Angle : 0.540 5.562 2476 Z= 0.290 Chirality : 0.046 0.147 290 Planarity : 0.005 0.036 320 Dihedral : 5.265 25.961 252 Min Nonbonded Distance : 2.643 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 : 0.56 (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 : 0.193 Fit side-chains REVERT: B 103 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8375 (tm) outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 1.4557 time to fit residues: 78.1905 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 : 0.179 ------------------------------------------------------------------------------- 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: 5.9990 chunk 13 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 8 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 11 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 = 0.3786 r_free = 0.3786 target = 0.152656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132517 restraints weight = 1834.707| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.77 r_work: 0.3476 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.2107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 1820 Z= 0.167 Angle : 0.497 5.385 2476 Z= 0.266 Chirality : 0.045 0.144 290 Planarity : 0.004 0.036 320 Dihedral : 4.808 24.240 252 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 6.99 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: 1.01 (0.56), residues: 230 helix: 1.91 (0.73), residues: 52 sheet: 0.32 (0.54), residues: 88 loop : 0.48 (0.69), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 32 PHE 0.009 0.001 PHE A 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 58 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.203 Fit side-chains REVERT: A 25 PHE cc_start: 0.8478 (t80) cc_final: 0.8141 (t80) outliers start: 5 outliers final: 3 residues processed: 54 average time/residue: 1.6724 time to fit residues: 91.6148 Evaluate side-chains 56 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.235 ------------------------------------------------------------------------------- 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 45 THR 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: 6.9990 chunk 17 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 2 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 = 0.3735 r_free = 0.3735 target = 0.148500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.128206 restraints weight = 1848.723| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 1.77 r_work: 0.3371 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 1820 Z= 0.323 Angle : 0.568 5.660 2476 Z= 0.303 Chirality : 0.047 0.147 290 Planarity : 0.005 0.037 320 Dihedral : 5.379 26.394 252 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.58 % Allowed : 17.01 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.86 (0.55), residues: 230 helix: 1.52 (0.72), residues: 52 sheet: 0.07 (0.56), residues: 78 loop : 0.69 (0.65), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 32 PHE 0.010 0.002 PHE B 4 TYR 0.008 0.002 TYR B 58 ARG 0.003 0.001 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 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.190 Fit side-chains REVERT: A 40 GLN cc_start: 0.8491 (tt0) cc_final: 0.8209 (mt0) REVERT: B 103 LEU cc_start: 0.8638 (OUTLIER) cc_final: 0.8438 (tm) outliers start: 5 outliers final: 2 residues processed: 50 average time/residue: 1.6622 time to fit residues: 84.1826 Evaluate side-chains 52 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 49 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 16 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 8.9990 chunk 6 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 overall best weight: 1.1582 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.152451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131858 restraints weight = 1872.708| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 1.82 r_work: 0.3473 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.2242 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= 0.167 Angle : 0.496 5.385 2476 Z= 0.265 Chirality : 0.045 0.143 290 Planarity : 0.004 0.036 320 Dihedral : 4.808 23.942 252 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.06 % Allowed : 18.56 % Favored : 79.38 % 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: 1.03 (0.56), residues: 230 helix: 1.87 (0.73), residues: 52 sheet: 0.05 (0.55), residues: 78 loop : 0.80 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 32 PHE 0.008 0.001 PHE A 4 TYR 0.008 0.001 TYR B 58 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 57 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 53 time to evaluate : 0.217 Fit side-chains REVERT: A 25 PHE cc_start: 0.8459 (t80) cc_final: 0.8135 (t80) REVERT: A 40 GLN cc_start: 0.8403 (tt0) cc_final: 0.8090 (mt0) outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 1.5726 time to fit residues: 86.0774 Evaluate side-chains 55 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 52 time to evaluate : 0.214 ------------------------------------------------------------------------------- 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 45 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 3 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.151012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130346 restraints weight = 1838.625| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.81 r_work: 0.3462 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3339 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2199 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= 0.193 Angle : 0.510 5.436 2476 Z= 0.271 Chirality : 0.045 0.141 290 Planarity : 0.005 0.038 320 Dihedral : 4.904 24.443 252 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % 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: 1.01 (0.56), residues: 230 helix: 1.81 (0.73), residues: 52 sheet: 0.30 (0.54), residues: 88 loop : 0.59 (0.69), residues: 90 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 0.009 0.001 TYR B 42 ARG 0.002 0.000 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 : 0.214 Fit side-chains REVERT: A 40 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.8105 (mt0) REVERT: B 89 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7777 (mm-30) outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 1.5471 time to fit residues: 83.1196 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 : 0.209 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 4 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 0 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 13 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.147744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.126989 restraints weight = 1878.544| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.82 r_work: 0.3369 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 1820 Z= 0.320 Angle : 0.571 5.644 2476 Z= 0.303 Chirality : 0.047 0.149 290 Planarity : 0.005 0.036 320 Dihedral : 5.365 26.473 252 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 3.09 % Allowed : 17.53 % Favored : 79.38 % 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: 0.85 (0.55), residues: 230 helix: 1.47 (0.71), residues: 52 sheet: 0.00 (0.55), residues: 78 loop : 0.77 (0.66), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP B 32 PHE 0.008 0.002 PHE A 4 TYR 0.009 0.002 TYR B 58 ARG 0.003 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 54 residues out of total 194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.197 Fit side-chains REVERT: A 40 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.8160 (mt0) REVERT: B 89 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7793 (mm-30) outliers start: 6 outliers final: 3 residues processed: 49 average time/residue: 1.5711 time to fit residues: 78.0315 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 : 0.199 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 89 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 22 random chunks: chunk 8 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 overall best weight: 1.0386 ------------------------------------------------------------------------------- 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 = 0.3773 r_free = 0.3773 target = 0.152165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.131798 restraints weight = 1872.091| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 1.80 r_work: 0.3477 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 1820 Z= 0.156 Angle : 0.500 5.343 2476 Z= 0.267 Chirality : 0.045 0.143 290 Planarity : 0.004 0.036 320 Dihedral : 4.809 24.135 252 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 2.58 % Allowed : 19.07 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.07 (0.55), residues: 230 helix: 1.90 (0.73), residues: 52 sheet: 0.05 (0.54), residues: 78 loop : 0.84 (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 B 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: 5 poor density : 52 time to evaluate : 0.234 Fit side-chains REVERT: A 40 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8089 (mt0) outliers start: 5 outliers final: 3 residues processed: 53 average time/residue: 1.6252 time to fit residues: 87.3026 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 : 0.208 ------------------------------------------------------------------------------- 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: 0.2980 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 overall best weight: 1.6588 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.151227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.130693 restraints weight = 1945.900| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 1.82 r_work: 0.3450 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.2333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 1820 Z= 0.203 Angle : 0.518 5.444 2476 Z= 0.275 Chirality : 0.045 0.142 290 Planarity : 0.005 0.038 320 Dihedral : 4.934 24.874 252 Min Nonbonded Distance : 2.660 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.87 % Favored : 99.13 % Rotamer: Outliers : 2.06 % Allowed : 19.59 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.83 (0.73), residues: 52 sheet: 0.29 (0.53), residues: 88 loop : 0.49 (0.67), residues: 90 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 0.009 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 : 0.196 Fit side-chains REVERT: A 40 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8108 (mt0) outliers start: 4 outliers final: 3 residues processed: 53 average time/residue: 1.5922 time to fit residues: 85.4709 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 : 0.169 ------------------------------------------------------------------------------- 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: 0.8980 chunk 14 optimal weight: 10.0000 chunk 4 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 6.9990 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 = 0.151376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131162 restraints weight = 1856.699| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.77 r_work: 0.3458 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2264 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= 0.208 Angle : 0.522 5.455 2476 Z= 0.278 Chirality : 0.045 0.143 290 Planarity : 0.005 0.037 320 Dihedral : 4.981 25.354 252 Min Nonbonded Distance : 2.659 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % 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: 0.96 (0.55), residues: 230 helix: 1.79 (0.73), residues: 52 sheet: 0.31 (0.53), residues: 88 loop : 0.47 (0.67), residues: 90 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 0.010 0.002 TYR B 42 ARG 0.003 0.001 ARG A 49 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.75 seconds wall clock time: 40 minutes 2.89 seconds (2402.89 seconds total)