Starting phenix.real_space_refine on Wed Mar 5 14:18:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6fu8_4319/03_2025/6fu8_4319_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6fu8_4319/03_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_4319/03_2025/6fu8_4319.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6fu8_4319/03_2025/6fu8_4319.map" model { file = "/net/cci-nas-00/data/ceres_data/6fu8_4319/03_2025/6fu8_4319_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6fu8_4319/03_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): 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 2.79, per 1000 atoms: 2.05 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 96.2 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: 0.41 Time building geometry restraints manager: 0.44 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: 3.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.730 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.650 ------------------------------------------------------------------------------- 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 : 0.119 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: 0.6745 time to fit residues: 17.3574 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 : 0.120 ------------------------------------------------------------------------------- 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: 6.9990 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 = 15500.064| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 8.52 r_work: 0.3790 rms_B_bonded: 8.18 restraints_weight: 2.0000 r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7068 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 : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASP cc_start: 0.8946 (m-30) cc_final: 0.8695 (m-30) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.4825 time to fit residues: 6.6533 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 : 0.130 ------------------------------------------------------------------------------- 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: 10.0000 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 overall best weight: 2.4990 ------------------------------------------------------------------------------- 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 = 0.4009 r_free = 0.4009 target = 0.072108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.065760 restraints weight = 16136.947| |-----------------------------------------------------------------------------| r_work (start): 0.4068 rms_B_bonded: 8.35 r_work (final): 0.4068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.7594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 658 Z= 0.209 Angle : 0.734 7.273 883 Z= 0.401 Chirality : 0.045 0.115 109 Planarity : 0.004 0.023 108 Dihedral : 8.079 51.169 88 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.75 % Favored : 90.00 % Rotamer: Outliers : 0.00 % Allowed : 22.22 % 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: -3.31 (0.76), residues: 80 helix: -1.02 (0.87), residues: 28 sheet: -1.44 (0.93), residues: 21 loop : -3.86 (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 0.001 0.000 PHE C 51 TYR 0.007 0.002 TYR C 73 ARG 0.002 0.000 ARG C 66 *********************** 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 13 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 68 ASP cc_start: 0.8703 (m-30) cc_final: 0.8412 (m-30) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.4400 time to fit residues: 6.0659 Evaluate side-chains 9 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.117 ------------------------------------------------------------------------------- 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: 9.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 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 = 0.3967 r_free = 0.3967 target = 0.073133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.066237 restraints weight = 16431.064| |-----------------------------------------------------------------------------| r_work (start): 0.3913 rms_B_bonded: 9.27 r_work (final): 0.3913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7248 moved from start: 0.8854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 658 Z= 0.216 Angle : 0.664 6.083 883 Z= 0.362 Chirality : 0.042 0.111 109 Planarity : 0.004 0.020 108 Dihedral : 6.775 37.156 88 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.75 % Favored : 90.00 % Rotamer: Outliers : 2.78 % Allowed : 22.22 % 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: -2.83 (0.87), residues: 80 helix: -0.32 (1.00), residues: 28 sheet: -1.48 (0.99), residues: 22 loop : -3.71 (0.92), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.003 TRP C 69 HIS 0.001 0.001 HIS C 15 PHE 0.003 0.001 PHE C 51 TYR 0.004 0.001 TYR C 73 ARG 0.007 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 9 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 7 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 68 ASP cc_start: 0.9165 (m-30) cc_final: 0.8909 (m-30) outliers start: 2 outliers final: 0 residues processed: 9 average time/residue: 0.2187 time to fit residues: 2.2537 Evaluate side-chains 7 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.123 ------------------------------------------------------------------------------- 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: 5.9990 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 8.9990 overall best weight: 2.7490 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.073131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.065287 restraints weight = 14967.657| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 9.26 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6395 moved from start: 0.9235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 658 Z= 0.160 Angle : 0.614 4.272 883 Z= 0.331 Chirality : 0.042 0.113 109 Planarity : 0.004 0.019 108 Dihedral : 5.696 23.060 88 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 1.25 % Allowed : 8.75 % Favored : 90.00 % 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: -2.45 (0.92), residues: 80 helix: 0.05 (1.04), residues: 28 sheet: -1.16 (1.05), residues: 21 loop : -3.58 (1.01), residues: 31 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 69 HIS 0.001 0.000 HIS C 15 PHE 0.001 0.000 PHE C 51 TYR 0.005 0.001 TYR C 73 ARG 0.003 0.000 ARG C 65 *********************** 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 : 0.122 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 10 average time/residue: 0.4435 time to fit residues: 4.7525 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 : 0.174 ------------------------------------------------------------------------------- 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: 0.1980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 overall best weight: 0.7983 ------------------------------------------------------------------------------- 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 = 0.4017 r_free = 0.4017 target = 0.073722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.066078 restraints weight = 14785.786| |-----------------------------------------------------------------------------| r_work (start): 0.3937 rms_B_bonded: 9.19 r_work: 0.3802 rms_B_bonded: 9.14 restraints_weight: 2.0000 r_work: 0.3891 rms_B_bonded: 5.23 restraints_weight: 4.0000 r_work (final): 0.3891 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.9447 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= 0.164 Angle : 0.617 4.943 883 Z= 0.323 Chirality : 0.042 0.115 109 Planarity : 0.004 0.024 108 Dihedral : 5.226 15.460 88 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 1.25 % Allowed : 10.00 % Favored : 88.75 % Rotamer: Outliers : 0.00 % Allowed : 23.61 % 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: -2.47 (0.93), residues: 80 helix: 0.15 (1.06), residues: 28 sheet: -1.56 (1.02), residues: 22 loop : -3.45 (1.03), residues: 30 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 0.004 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: 0 poor density : 10 time to evaluate : 0.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: 0.0466 (mmt) cc_final: -0.0158 (mmt) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.4302 time to fit residues: 4.6159 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 : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 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 = 0.3964 r_free = 0.3964 target = 0.072484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.065386 restraints weight = 15580.112| |-----------------------------------------------------------------------------| r_work (start): 0.3851 rms_B_bonded: 9.28 r_work (final): 0.3851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.9993 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= 0.191 Angle : 0.595 5.249 883 Z= 0.319 Chirality : 0.042 0.109 109 Planarity : 0.004 0.020 108 Dihedral : 5.158 15.585 88 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 1.25 % Allowed : 11.25 % Favored : 87.50 % Rotamer: Outliers : 1.39 % Allowed : 25.00 % 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: -2.60 (0.91), residues: 80 helix: -0.17 (1.02), residues: 29 sheet: -1.04 (1.09), residues: 21 loop : -3.86 (0.93), residues: 30 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 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 0.001 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 9 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 8 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1 MET cc_start: -0.4431 (mmt) cc_final: -0.4709 (mmt) outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.4913 time to fit residues: 4.7429 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 : 0.125 ------------------------------------------------------------------------------- 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: 6.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 overall best weight: 6.2490 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.075161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.068011 restraints weight = 16215.368| |-----------------------------------------------------------------------------| r_work (start): 0.4054 rms_B_bonded: 9.72 r_work (final): 0.4054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 1.0873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 658 Z= 0.243 Angle : 0.663 6.058 883 Z= 0.357 Chirality : 0.043 0.110 109 Planarity : 0.005 0.026 108 Dihedral : 5.714 20.819 88 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 1.25 % Allowed : 10.00 % Favored : 88.75 % Rotamer: Outliers : 1.39 % Allowed : 25.00 % 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: -3.30 (0.86), residues: 80 helix: -1.08 (0.95), residues: 29 sheet: -1.20 (1.09), residues: 22 loop : -4.14 (0.85), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 69 HIS 0.003 0.002 HIS C 15 PHE 0.007 0.002 PHE C 51 TYR 0.004 0.002 TYR C 73 ARG 0.004 0.001 ARG C 66 *********************** 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 7 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 7 average time/residue: 0.3635 time to fit residues: 2.8125 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 : 0.116 ------------------------------------------------------------------------------- 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: 4.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 7.9990 overall best weight: 2.2235 ------------------------------------------------------------------------------- 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 = 0.4059 r_free = 0.4059 target = 0.074942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.068117 restraints weight = 15688.486| |-----------------------------------------------------------------------------| r_work (start): 0.4071 rms_B_bonded: 9.38 r_work (final): 0.4071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 1.0933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 658 Z= 0.145 Angle : 0.601 5.726 883 Z= 0.315 Chirality : 0.043 0.113 109 Planarity : 0.004 0.030 108 Dihedral : 5.021 12.428 88 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 1.25 % Allowed : 11.25 % Favored : 87.50 % Rotamer: Outliers : 1.39 % Allowed : 25.00 % 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: -2.96 (0.88), residues: 80 helix: -0.60 (1.01), residues: 29 sheet: -0.95 (1.11), residues: 21 loop : -4.17 (0.82), 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 0.002 0.001 PHE C 51 TYR 0.006 0.002 TYR C 73 ARG 0.002 0.000 ARG C 66 *********************** 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 7 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 6 time to evaluate : 0.120 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 7 average time/residue: 0.3783 time to fit residues: 2.9184 Evaluate side-chains 5 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.118 ------------------------------------------------------------------------------- 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: 1.9990 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 overall best weight: 2.4990 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.076718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.069913 restraints weight = 15972.419| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 9.24 r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 1.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 658 Z= 0.171 Angle : 0.653 7.753 883 Z= 0.334 Chirality : 0.043 0.109 109 Planarity : 0.004 0.034 108 Dihedral : 5.263 16.394 88 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 1.25 % Allowed : 10.00 % Favored : 88.75 % Rotamer: Outliers : 0.00 % Allowed : 29.17 % 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: -2.94 (0.89), residues: 80 helix: -0.62 (1.02), residues: 29 sheet: -1.16 (1.10), residues: 22 loop : -3.98 (0.83), residues: 29 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 69 HIS 0.002 0.001 HIS C 15 PHE 0.003 0.001 PHE C 51 TYR 0.004 0.001 TYR C 73 ARG 0.001 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 4 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.132 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.1692 time to fit residues: 0.9044 Evaluate side-chains 3 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 8.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 overall best weight: 1.6985 ------------------------------------------------------------------------------- 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 = 0.4063 r_free = 0.4063 target = 0.074772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.068635 restraints weight = 15784.511| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 8.73 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7161 moved from start: 1.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 658 Z= 0.156 Angle : 0.634 6.388 883 Z= 0.325 Chirality : 0.042 0.112 109 Planarity : 0.004 0.031 108 Dihedral : 4.826 12.319 88 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 1.25 % Allowed : 10.00 % Favored : 88.75 % Rotamer: Outliers : 0.00 % Allowed : 29.17 % 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: -2.57 (0.90), residues: 80 helix: -0.37 (1.06), residues: 28 sheet: -0.52 (1.21), residues: 19 loop : -3.72 (0.82), residues: 33 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 69 HIS 0.001 0.001 HIS C 15 PHE 0.002 0.000 PHE C 51 TYR 0.006 0.002 TYR C 73 ARG 0.002 0.000 ARG C 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1492.33 seconds wall clock time: 26 minutes 22.58 seconds (1582.58 seconds total)