Starting phenix.real_space_refine on Mon Feb 10 19:28:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fu8_4319/02_2025/6fu8_4319_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fu8_4319/02_2025/6fu8_4319.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6fu8_4319/02_2025/6fu8_4319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fu8_4319/02_2025/6fu8_4319.map" model { file = "/net/cci-nas-00/data/ceres_data/6fu8_4319/02_2025/6fu8_4319_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fu8_4319/02_2025/6fu8_4319_neut.cif" } resolution = 3.2 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= -0.010 sd= 0.125 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: 5 Type Number sf(0) Gaussians S 2 5.16 5 C 414 2.51 5 N 117 2.21 5 O 120 1.98 5 H 711 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 1364 Number of models: 1 Model: "" Number of chains: 1 Chain: "C" Number of atoms: 1364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 1364 Classifications: {'peptide': 82} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Time building chain proxies: 3.65, per 1000 atoms: 2.68 Number of scatterers: 1364 At special positions: 0 Unit cell: (50.14, 55.59, 39.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 2 16.00 O 120 8.00 N 117 7.00 C 414 6.00 H 711 1.00 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: 0.35 Conformation dependent library (CDL) restraints added in 76.1 milliseconds 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 162 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 1 sheets defined 39.0% alpha, 25.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'C' and resid 3 through 10 removed outlier: 3.983A pdb=" N LEU C 7 " --> pdb=" O ARG C 3 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS C 9 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 28 removed outlier: 3.572A pdb=" N MET C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 39 through 51 Processing sheet with id=AA1, first strand: chain 'C' and resid 11 through 14 removed outlier: 6.638A pdb=" N LYS C 33 " --> pdb=" O ARG C 12 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL C 31 " --> pdb=" O PRO C 14 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS C 70 " --> pdb=" O VAL C 34 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N VAL C 57 " --> pdb=" O THR C 75 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 84 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: 0.42 Time building geometry restraints manager: 0.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.13: 711 1.13 - 1.30: 116 1.30 - 1.48: 203 1.48 - 1.65: 335 1.65 - 1.82: 4 Bond restraints: 1369 Sorted by residual: bond pdb=" NH2 ARG C 6 " pdb="HH21 ARG C 6 " ideal model delta sigma weight residual 0.860 1.026 -0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" N LYS C 19 " pdb=" H LYS C 19 " ideal model delta sigma weight residual 0.860 1.025 -0.165 2.00e-02 2.50e+03 6.82e+01 bond pdb=" N GLU C 56 " pdb=" H GLU C 56 " ideal model delta sigma weight residual 0.860 1.024 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" N LEU C 8 " pdb=" H LEU C 8 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N THR C 75 " pdb=" H THR C 75 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.61e+01 ... (remaining 1364 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 1717 1.84 - 3.68: 546 3.68 - 5.53: 160 5.53 - 7.37: 64 7.37 - 9.21: 19 Bond angle restraints: 2506 Sorted by residual: angle pdb=" OE1 GLN C 48 " pdb=" CD GLN C 48 " pdb=" NE2 GLN C 48 " ideal model delta sigma weight residual 122.60 115.59 7.01 1.00e+00 1.00e+00 4.91e+01 angle pdb=" C GLU C 78 " pdb=" N GLY C 79 " pdb=" CA GLY C 79 " ideal model delta sigma weight residual 122.18 126.72 -4.54 6.90e-01 2.10e+00 4.33e+01 angle pdb=" CA ASN C 81 " pdb=" CB ASN C 81 " pdb=" CG ASN C 81 " ideal model delta sigma weight residual 112.60 118.35 -5.75 1.00e+00 1.00e+00 3.31e+01 angle pdb=" C SER C 67 " pdb=" N ASP C 68 " pdb=" CA ASP C 68 " ideal model delta sigma weight residual 122.82 129.68 -6.86 1.42e+00 4.96e-01 2.33e+01 angle pdb=" C LEU C 32 " pdb=" N LYS C 33 " pdb=" CA LYS C 33 " ideal model delta sigma weight residual 122.42 128.49 -6.07 1.33e+00 5.65e-01 2.08e+01 ... (remaining 2501 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 17.65: 550 17.65 - 35.29: 33 35.29 - 52.93: 14 52.93 - 70.57: 11 70.57 - 88.21: 9 Dihedral angle restraints: 617 sinusoidal: 355 harmonic: 262 Sorted by residual: dihedral pdb=" CA ALA C 13 " pdb=" C ALA C 13 " pdb=" N PRO C 14 " pdb=" CA PRO C 14 " ideal model delta harmonic sigma weight residual 180.00 149.98 30.02 0 5.00e+00 4.00e-02 3.60e+01 dihedral pdb=" CA ALA C 38 " pdb=" C ALA C 38 " pdb=" N THR C 39 " pdb=" CA THR C 39 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA LYS C 26 " pdb=" C LYS C 26 " pdb=" N SER C 27 " pdb=" CA SER C 27 " ideal model delta harmonic sigma weight residual 180.00 -157.07 -22.93 0 5.00e+00 4.00e-02 2.10e+01 ... (remaining 614 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 66 0.076 - 0.151: 32 0.151 - 0.226: 5 0.226 - 0.301: 3 0.301 - 0.377: 3 Chirality restraints: 109 Sorted by residual: chirality pdb=" CA MET C 1 " pdb=" N MET C 1 " pdb=" C MET C 1 " pdb=" CB MET C 1 " both_signs ideal model delta sigma weight residual False 2.57 2.19 0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" CA ASP C 68 " pdb=" N ASP C 68 " pdb=" C ASP C 68 " pdb=" CB ASP C 68 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASN C 81 " pdb=" N ASN C 81 " pdb=" C ASN C 81 " pdb=" CB ASN C 81 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 106 not shown) Planarity restraints: 188 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 69 " 0.451 2.00e-02 2.50e+03 1.46e-01 8.58e+02 pdb=" CG TRP C 69 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TRP C 69 " -0.195 2.00e-02 2.50e+03 pdb=" CD2 TRP C 69 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP C 69 " -0.117 2.00e-02 2.50e+03 pdb=" CE2 TRP C 69 " -0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP C 69 " -0.069 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 69 " 0.066 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 69 " -0.045 2.00e-02 2.50e+03 pdb=" CH2 TRP C 69 " 0.046 2.00e-02 2.50e+03 pdb=" HD1 TRP C 69 " -0.148 2.00e-02 2.50e+03 pdb=" HE1 TRP C 69 " 0.095 2.00e-02 2.50e+03 pdb=" HE3 TRP C 69 " -0.094 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 69 " 0.126 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 69 " -0.092 2.00e-02 2.50e+03 pdb=" HH2 TRP C 69 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 12 " 0.364 9.50e-02 1.11e+02 1.71e-01 3.39e+02 pdb=" NE ARG C 12 " 0.098 2.00e-02 2.50e+03 pdb=" CZ ARG C 12 " 0.071 2.00e-02 2.50e+03 pdb=" NH1 ARG C 12 " 0.121 2.00e-02 2.50e+03 pdb=" NH2 ARG C 12 " 0.007 2.00e-02 2.50e+03 pdb="HH11 ARG C 12 " -0.201 2.00e-02 2.50e+03 pdb="HH12 ARG C 12 " -0.026 2.00e-02 2.50e+03 pdb="HH21 ARG C 12 " -0.209 2.00e-02 2.50e+03 pdb="HH22 ARG C 12 " 0.124 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 6 " -0.345 9.50e-02 1.11e+02 1.51e-01 2.27e+02 pdb=" NE ARG C 6 " -0.102 2.00e-02 2.50e+03 pdb=" CZ ARG C 6 " -0.021 2.00e-02 2.50e+03 pdb=" NH1 ARG C 6 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG C 6 " 0.033 2.00e-02 2.50e+03 pdb="HH11 ARG C 6 " 0.072 2.00e-02 2.50e+03 pdb="HH12 ARG C 6 " 0.044 2.00e-02 2.50e+03 pdb="HH21 ARG C 6 " 0.174 2.00e-02 2.50e+03 pdb="HH22 ARG C 6 " -0.191 2.00e-02 2.50e+03 ... (remaining 185 not shown) Histogram of nonbonded interaction distances: 1.67 - 2.26: 142 2.26 - 2.84: 2788 2.84 - 3.43: 3520 3.43 - 4.01: 4570 4.01 - 4.60: 6525 Nonbonded interactions: 17545 Sorted by model distance: nonbonded pdb=" O SER C 27 " pdb=" HG1 THR C 29 " model vdw 1.671 2.450 nonbonded pdb=" HE ARG C 6 " pdb=" OE2 GLU C 42 " model vdw 1.718 2.450 nonbonded pdb=" O ASP C 37 " pdb=" HZ3 LYS C 70 " model vdw 1.722 2.450 nonbonded pdb="HG12 VAL C 62 " pdb=" H LYS C 64 " model vdw 1.727 2.270 nonbonded pdb=" OG1 THR C 29 " pdb=" HG1 THR C 75 " model vdw 1.747 2.450 ... (remaining 17540 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.510 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: 0.020 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.670 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4282 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.038 658 Z= 0.862 Angle : 2.112 7.412 883 Z= 1.370 Chirality : 0.103 0.377 109 Planarity : 0.021 0.145 108 Dihedral : 20.182 88.210 259 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.47 Ramachandran Plot: Outliers : 2.50 % Allowed : 11.25 % Favored : 86.25 % Rotamer: Outliers : 2.78 % Allowed : 18.06 % Favored : 79.17 % Cbeta Deviations : 2.47 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 100.00 % 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: -3.87 (0.78), residues: 80 helix: -2.54 (0.87), residues: 28 sheet: -3.18 (1.11), residues: 14 loop : -2.21 (0.81), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.299 0.122 TRP C 69 HIS 0.011 0.007 HIS C 15 PHE 0.014 0.007 PHE C 51 TYR 0.035 0.017 TYR C 73 ARG 0.008 0.002 ARG C 3 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 0.6794 time to fit residues: 17.4792 Evaluate side-chains 12 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 = 0.3989 r_free = 0.3989 target = 0.072367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.066041 restraints weight = 15500.018| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 8.52 r_work: 0.3789 rms_B_bonded: 8.17 restraints_weight: 2.0000 r_work (final): 0.3789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7069 moved from start: 0.6544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 658 Z= 0.299 Angle : 0.838 6.062 883 Z= 0.459 Chirality : 0.046 0.110 109 Planarity : 0.005 0.021 108 Dihedral : 9.348 64.439 88 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 1.25 % Allowed : 6.25 % Favored : 92.50 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % 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: -3.48 (0.76), residues: 80 helix: -0.95 (0.96), residues: 28 sheet: -1.80 (0.85), residues: 21 loop : -3.96 (0.72), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP C 69 HIS 0.004 0.002 HIS C 15 PHE 0.007 0.002 PHE C 51 TYR 0.006 0.002 TYR C 73 ARG 0.005 0.001 ARG C 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASP cc_start: 0.8949 (m-30) cc_final: 0.8702 (m-30) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.4851 time to fit residues: 6.6558 Evaluate side-chains 10 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 overall best weight: 4.7490 ------------------------------------------------------------------------------- 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 = 0.4006 r_free = 0.4006 target = 0.072803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.065950 restraints weight = 16195.455| |-----------------------------------------------------------------------------| r_work (start): 0.4066 rms_B_bonded: 8.78 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.7865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 658 Z= 0.249 Angle : 0.744 7.174 883 Z= 0.412 Chirality : 0.045 0.114 109 Planarity : 0.004 0.021 108 Dihedral : 8.095 50.800 88 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.75 % Favored : 90.00 % Rotamer: Outliers : 1.39 % Allowed : 20.83 % Favored : 77.78 % 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: -3.46 (0.76), residues: 80 helix: -1.25 (0.84), residues: 28 sheet: -1.42 (0.96), residues: 21 loop : -3.91 (0.79), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP C 69 HIS 0.001 0.001 HIS C 15 PHE 0.002 0.001 PHE C 51 TYR 0.007 0.002 TYR C 73 ARG 0.001 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASP cc_start: 0.8912 (m-30) cc_final: 0.8623 (m-30) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.4297 time to fit residues: 6.3764 Evaluate side-chains 10 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 overall best weight: 2.9488 ------------------------------------------------------------------------------- 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 = 0.3962 r_free = 0.3962 target = 0.071008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.064785 restraints weight = 15278.167| |-----------------------------------------------------------------------------| r_work (start): 0.3891 rms_B_bonded: 8.60 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6422 moved from start: 0.8964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 658 Z= 0.186 Angle : 0.673 6.224 883 Z= 0.358 Chirality : 0.043 0.119 109 Planarity : 0.004 0.020 108 Dihedral : 6.384 34.416 88 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 1.25 % Allowed : 10.00 % Favored : 88.75 % Rotamer: Outliers : 1.39 % Allowed : 23.61 % Favored : 75.00 % 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: -2.72 (0.88), residues: 80 helix: -0.20 (1.03), residues: 28 sheet: -1.48 (1.01), residues: 22 loop : -3.62 (0.92), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 69 HIS 0.001 0.001 HIS C 15 PHE 0.001 0.000 PHE C 51 TYR 0.005 0.001 TYR C 73 ARG 0.008 0.001 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 0.3885 time to fit residues: 4.9791 Evaluate side-chains 11 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 overall best weight: 4.4990 ------------------------------------------------------------------------------- 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 = 0.3999 r_free = 0.3999 target = 0.072822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.065798 restraints weight = 15866.880| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 8.95 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 moved from start: 0.9543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 658 Z= 0.208 Angle : 0.613 4.418 883 Z= 0.334 Chirality : 0.042 0.110 109 Planarity : 0.005 0.031 108 Dihedral : 5.708 19.646 88 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 1.25 % Allowed : 10.00 % Favored : 88.75 % Rotamer: Outliers : 1.39 % Allowed : 22.22 % Favored : 76.39 % 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: -2.67 (0.92), residues: 80 helix: -0.34 (1.01), residues: 29 sheet: -1.15 (1.07), residues: 21 loop : -3.71 (1.06), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP C 69 HIS 0.001 0.001 HIS C 15 PHE 0.004 0.001 PHE C 51 TYR 0.003 0.001 TYR C 73 ARG 0.002 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: -0.4263 (mmt) cc_final: -0.4481 (mmt) outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.4476 time to fit residues: 4.8001 Evaluate side-chains 10 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 = 0.3949 r_free = 0.3949 target = 0.072196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.065048 restraints weight = 16329.515| |-----------------------------------------------------------------------------| r_work (start): 0.3847 rms_B_bonded: 9.64 r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6375 moved from start: 0.9905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 658 Z= 0.165 Angle : 0.611 4.951 883 Z= 0.322 Chirality : 0.042 0.109 109 Planarity : 0.004 0.022 108 Dihedral : 4.982 16.494 88 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 1.25 % Allowed : 10.00 % Favored : 88.75 % Rotamer: Outliers : 1.39 % Allowed : 22.22 % Favored : 76.39 % 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: -2.68 (0.91), residues: 80 helix: -0.20 (1.02), residues: 29 sheet: -1.42 (1.05), residues: 22 loop : -3.72 (0.97), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP C 69 HIS 0.001 0.001 HIS C 15 PHE 0.001 0.000 PHE C 51 TYR 0.003 0.001 TYR C 73 ARG 0.002 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.4699 time to fit residues: 4.9993 Evaluate side-chains 10 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 overall best weight: 4.2238 ------------------------------------------------------------------------------- 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 = 0.3986 r_free = 0.3986 target = 0.073446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.066070 restraints weight = 16027.449| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 9.52 r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6367 moved from start: 1.0413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 658 Z= 0.194 Angle : 0.600 5.094 883 Z= 0.320 Chirality : 0.042 0.107 109 Planarity : 0.005 0.024 108 Dihedral : 5.058 12.194 88 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 1.25 % Allowed : 10.00 % Favored : 88.75 % Rotamer: Outliers : 2.78 % Allowed : 23.61 % Favored : 73.61 % 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: -2.79 (0.90), residues: 80 helix: -0.40 (1.00), residues: 29 sheet: -1.13 (1.09), residues: 21 loop : -3.89 (0.94), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 69 HIS 0.002 0.001 HIS C 15 PHE 0.004 0.001 PHE C 51 TYR 0.003 0.001 TYR C 73 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 8 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 10 average time/residue: 0.2972 time to fit residues: 3.2873 Evaluate side-chains 8 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 7 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 4.2490 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.073886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.066828 restraints weight = 15660.414| |-----------------------------------------------------------------------------| r_work (start): 0.4059 rms_B_bonded: 9.25 r_work (final): 0.4059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 1.0749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 658 Z= 0.180 Angle : 0.644 5.315 883 Z= 0.341 Chirality : 0.041 0.107 109 Planarity : 0.004 0.024 108 Dihedral : 5.005 16.530 88 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 1.25 % Allowed : 10.00 % Favored : 88.75 % Rotamer: Outliers : 1.39 % Allowed : 22.22 % Favored : 76.39 % 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: -2.94 (0.88), residues: 80 helix: -0.61 (0.99), residues: 29 sheet: -1.31 (1.07), residues: 22 loop : -3.86 (0.89), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 69 HIS 0.002 0.001 HIS C 15 PHE 0.003 0.001 PHE C 51 TYR 0.003 0.001 TYR C 73 ARG 0.001 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.3059 time to fit residues: 3.3713 Evaluate side-chains 8 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 7 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- 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 = 0.4053 r_free = 0.4053 target = 0.075989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.068276 restraints weight = 15724.260| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 9.54 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7171 moved from start: 1.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 658 Z= 0.169 Angle : 0.663 5.958 883 Z= 0.349 Chirality : 0.041 0.111 109 Planarity : 0.004 0.024 108 Dihedral : 4.854 13.149 88 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.75 % Favored : 90.00 % Rotamer: Outliers : 1.39 % Allowed : 26.39 % Favored : 72.22 % 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: -2.85 (0.88), residues: 80 helix: -0.43 (1.03), residues: 29 sheet: -1.08 (1.08), residues: 21 loop : -4.03 (0.81), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 69 HIS 0.002 0.001 HIS C 15 PHE 0.002 0.001 PHE C 51 TYR 0.004 0.001 TYR C 73 ARG 0.001 0.000 ARG C 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 8 time to evaluate : 0.120 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.5207 time to fit residues: 5.0084 Evaluate side-chains 7 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 overall best weight: 3.7490 ------------------------------------------------------------------------------- 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 = 0.4038 r_free = 0.4038 target = 0.075241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.067940 restraints weight = 16542.638| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 9.72 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 1.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 658 Z= 0.213 Angle : 0.730 7.706 883 Z= 0.380 Chirality : 0.043 0.111 109 Planarity : 0.004 0.024 108 Dihedral : 5.042 15.374 88 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.75 % Favored : 90.00 % Rotamer: Outliers : 1.39 % Allowed : 27.78 % Favored : 70.83 % 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: -3.09 (0.89), residues: 80 helix: -0.60 (1.02), residues: 29 sheet: -1.25 (1.09), residues: 22 loop : -4.24 (0.85), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 69 HIS 0.002 0.001 HIS C 15 PHE 0.003 0.001 PHE C 51 TYR 0.003 0.001 TYR C 73 ARG 0.002 0.000 ARG C 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 160 Ramachandran restraints generated. 80 Oldfield, 0 Emsley, 80 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 7 time to evaluate : 0.109 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 8 average time/residue: 0.5252 time to fit residues: 4.4890 Evaluate side-chains 8 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 7 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 18 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 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 = 0.4045 r_free = 0.4045 target = 0.075102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.067781 restraints weight = 15854.616| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 9.22 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 1.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 658 Z= 0.168 Angle : 0.677 6.145 883 Z= 0.353 Chirality : 0.042 0.111 109 Planarity : 0.004 0.025 108 Dihedral : 4.818 13.278 88 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.75 % Favored : 90.00 % Rotamer: Outliers : 1.39 % Allowed : 27.78 % Favored : 70.83 % 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: -2.70 (0.92), residues: 80 helix: -0.61 (1.03), residues: 29 sheet: -0.40 (1.23), residues: 19 loop : -3.89 (0.87), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP C 69 HIS 0.001 0.001 HIS C 15 PHE 0.002 0.001 PHE C 51 TYR 0.005 0.001 TYR C 73 ARG 0.002 0.000 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1437.25 seconds wall clock time: 26 minutes 3.52 seconds (1563.52 seconds total)