Starting phenix.real_space_refine on Tue Jan 13 09:54:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zqe_14872/01_2026/7zqe_14872.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zqe_14872/01_2026/7zqe_14872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.55 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zqe_14872/01_2026/7zqe_14872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zqe_14872/01_2026/7zqe_14872.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zqe_14872/01_2026/7zqe_14872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zqe_14872/01_2026/7zqe_14872.map" } resolution = 2.55 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.000 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: 6 Type Number sf(0) Gaussians Cu 1 5.60 5 S 2 5.16 5 C 459 2.51 5 N 118 2.21 5 O 149 1.98 5 H 694 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1423 Number of models: 1 Model: "" Number of chains: 2 Chain: "M" Number of atoms: 1422 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1422 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 92} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CU': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1197 SG CYS M 83 22.202 21.040 12.108 1.00 69.77 S Time building chain proxies: 0.27, per 1000 atoms: 0.19 Number of scatterers: 1423 At special positions: 0 Unit cell: (47.04, 39.48, 45.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cu 1 28.99 S 2 16.00 O 149 8.00 N 118 7.00 C 459 6.00 H 694 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: 0.09 Conformation dependent library (CDL) restraints added in 22.9 milliseconds 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 174 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 2 sheets defined 7.1% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'M' and resid 84 through 90 removed outlier: 5.271A pdb=" N GLY M 88 " --> pdb=" O PRO M 85 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'M' and resid 15 through 16 Processing sheet with id=AA2, first strand: chain 'M' and resid 19 through 23 removed outlier: 3.619A pdb=" N TYR M 82 " --> pdb=" O VAL M 41 " (cutoff:3.500A) 25 hydrogen bonds defined for protein. 57 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: 0.16 Time building geometry restraints manager: 0.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 694 1.03 - 1.23: 0 1.23 - 1.42: 315 1.42 - 1.61: 425 1.61 - 1.81: 3 Bond restraints: 1437 Sorted by residual: bond pdb=" N ASP M 1 " pdb=" CA ASP M 1 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.88e+00 bond pdb=" N ASP M 1 " pdb=" H ASP M 1 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" CB PRO M 37 " pdb=" CG PRO M 37 " ideal model delta sigma weight residual 1.506 1.481 0.025 3.90e-02 6.57e+02 3.96e-01 bond pdb=" CG PRO M 48 " pdb=" CD PRO M 48 " ideal model delta sigma weight residual 1.503 1.524 -0.021 3.40e-02 8.65e+02 3.93e-01 bond pdb=" CB PRO M 17 " pdb=" CG PRO M 17 " ideal model delta sigma weight residual 1.506 1.485 0.021 3.90e-02 6.57e+02 2.77e-01 ... (remaining 1432 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.91: 2411 0.91 - 1.81: 171 1.81 - 2.72: 7 2.72 - 3.63: 2 3.63 - 4.53: 3 Bond angle restraints: 2594 Sorted by residual: angle pdb=" CA ASP M 1 " pdb=" N ASP M 1 " pdb=" H ASP M 1 " ideal model delta sigma weight residual 114.00 109.47 4.53 3.00e+00 1.11e-01 2.28e+00 angle pdb=" N PRO M 37 " pdb=" CA PRO M 37 " pdb=" C PRO M 37 " ideal model delta sigma weight residual 112.10 116.01 -3.91 2.60e+00 1.48e-01 2.26e+00 angle pdb=" O PRO M 37 " pdb=" C PRO M 37 " pdb=" N HIS M 38 " ideal model delta sigma weight residual 121.10 123.61 -2.51 1.90e+00 2.77e-01 1.74e+00 angle pdb=" O PRO M 17 " pdb=" C PRO M 17 " pdb=" N LYS M 18 " ideal model delta sigma weight residual 121.10 123.20 -2.10 1.90e+00 2.77e-01 1.22e+00 angle pdb=" N PRO M 48 " pdb=" CD PRO M 48 " pdb=" HD2 PRO M 48 " ideal model delta sigma weight residual 109.00 112.17 -3.17 3.00e+00 1.11e-01 1.11e+00 ... (remaining 2589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.52: 622 11.52 - 23.03: 48 23.03 - 34.55: 10 34.55 - 46.07: 7 46.07 - 57.58: 1 Dihedral angle restraints: 688 sinusoidal: 366 harmonic: 322 Sorted by residual: dihedral pdb=" CA PHE M 36 " pdb=" C PHE M 36 " pdb=" N PRO M 37 " pdb=" CA PRO M 37 " ideal model delta harmonic sigma weight residual 0.00 14.36 -14.36 0 5.00e+00 4.00e-02 8.25e+00 dihedral pdb=" N ARG M 58 " pdb=" CA ARG M 58 " pdb=" CB ARG M 58 " pdb=" CG ARG M 58 " ideal model delta sinusoidal sigma weight residual -60.00 -95.29 35.29 3 1.50e+01 4.44e-03 6.04e+00 dihedral pdb=" CA GLY M 77 " pdb=" C GLY M 77 " pdb=" N GLU M 78 " pdb=" CA GLU M 78 " ideal model delta harmonic sigma weight residual 180.00 168.27 11.73 0 5.00e+00 4.00e-02 5.50e+00 ... (remaining 685 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.032: 72 0.032 - 0.063: 23 0.063 - 0.094: 5 0.094 - 0.125: 12 0.125 - 0.156: 1 Chirality restraints: 113 Sorted by residual: chirality pdb=" CA ILE M 47 " pdb=" N ILE M 47 " pdb=" C ILE M 47 " pdb=" CB ILE M 47 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.10e-01 chirality pdb=" CA ILE M 96 " pdb=" N ILE M 96 " pdb=" C ILE M 96 " pdb=" CB ILE M 96 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 chirality pdb=" CA ILE M 40 " pdb=" N ILE M 40 " pdb=" C ILE M 40 " pdb=" CB ILE M 40 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.44e-01 ... (remaining 110 not shown) Planarity restraints: 228 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE M 47 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.73e+00 pdb=" N PRO M 48 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO M 48 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO M 48 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY M 77 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C GLY M 77 " 0.032 2.00e-02 2.50e+03 pdb=" O GLY M 77 " -0.012 2.00e-02 2.50e+03 pdb=" N GLU M 78 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE M 30 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.03e+00 pdb=" C PHE M 30 " -0.025 2.00e-02 2.50e+03 pdb=" O PHE M 30 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL M 31 " 0.008 2.00e-02 2.50e+03 ... (remaining 225 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.25: 148 2.25 - 2.84: 3268 2.84 - 3.42: 3580 3.42 - 4.01: 5221 4.01 - 4.60: 7594 Nonbonded interactions: 19811 Sorted by model distance: nonbonded pdb=" O ALA M 75 " pdb=" HH TYR M 79 " model vdw 1.662 2.450 nonbonded pdb=" O ALA M 53 " pdb=" HG SER M 57 " model vdw 1.667 2.450 nonbonded pdb=" H SER M 24 " pdb=" O GLN M 98 " model vdw 1.682 2.450 nonbonded pdb=" O ILE M 40 " pdb=" H ARG M 58 " model vdw 1.736 2.450 nonbonded pdb=" O ALA M 34 " pdb=" HE2 HIS M 38 " model vdw 1.775 2.450 ... (remaining 19806 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: 16.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.280 Find NCS groups from input model: 0.000 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:4.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5031 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 : 0.002 0.032 743 Z= 0.103 Angle : 0.423 4.143 1012 Z= 0.222 Chirality : 0.048 0.156 113 Planarity : 0.006 0.054 136 Dihedral : 7.036 36.617 261 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.73 (0.85), residues: 96 helix: None (None), residues: 0 sheet: -0.70 (0.88), residues: 35 loop : -0.26 (0.80), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG M 58 TYR 0.001 0.000 TYR M 79 PHE 0.004 0.001 PHE M 15 HIS 0.003 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 743) covalent geometry : angle 0.42305 ( 1012) hydrogen bonds : bond 0.16946 ( 25) hydrogen bonds : angle 7.76065 ( 57) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.036 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 1.1218 time to fit residues: 12.4583 Evaluate side-chains 4 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 7 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 overall best weight: 0.5730 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.057501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.054112 restraints weight = 21879.189| |-----------------------------------------------------------------------------| r_work (start): 0.4382 rms_B_bonded: 3.85 r_work: 0.4312 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.4312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5335 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 743 Z= 0.106 Angle : 0.487 4.163 1012 Z= 0.250 Chirality : 0.046 0.146 113 Planarity : 0.006 0.046 136 Dihedral : 4.708 30.439 104 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 1.32 % Allowed : 5.26 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.33 (0.86), residues: 96 helix: None (None), residues: 0 sheet: -0.54 (0.87), residues: 35 loop : 0.10 (0.82), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG M 58 TYR 0.004 0.001 TYR M 79 PHE 0.006 0.001 PHE M 36 HIS 0.002 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 743) covalent geometry : angle 0.48750 ( 1012) hydrogen bonds : bond 0.02698 ( 25) hydrogen bonds : angle 5.53561 ( 57) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 4 time to evaluate : 0.040 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 5 average time/residue: 0.2970 time to fit residues: 1.5855 Evaluate side-chains 4 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.057895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.054814 restraints weight = 22242.931| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 3.75 r_work: 0.4300 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5355 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 743 Z= 0.106 Angle : 0.467 4.209 1012 Z= 0.241 Chirality : 0.046 0.149 113 Planarity : 0.005 0.043 136 Dihedral : 4.926 35.599 104 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.88), residues: 96 helix: None (None), residues: 0 sheet: -0.14 (0.86), residues: 35 loop : 0.08 (0.85), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG M 58 TYR 0.006 0.001 TYR M 79 PHE 0.007 0.001 PHE M 15 HIS 0.002 0.001 HIS M 86 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 743) covalent geometry : angle 0.46661 ( 1012) hydrogen bonds : bond 0.02095 ( 25) hydrogen bonds : angle 4.41531 ( 57) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.2837 time to fit residues: 1.2030 Evaluate side-chains 3 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.8233 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.057641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.054479 restraints weight = 22257.097| |-----------------------------------------------------------------------------| r_work (start): 0.4359 rms_B_bonded: 3.87 r_work: 0.4296 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5468 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 743 Z= 0.113 Angle : 0.464 4.241 1012 Z= 0.242 Chirality : 0.046 0.146 113 Planarity : 0.005 0.041 136 Dihedral : 4.952 34.895 104 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.88), residues: 96 helix: None (None), residues: 0 sheet: -0.35 (0.86), residues: 37 loop : 0.15 (0.86), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.002 ARG M 58 TYR 0.005 0.001 TYR M 61 PHE 0.009 0.002 PHE M 15 HIS 0.002 0.001 HIS M 86 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 743) covalent geometry : angle 0.46391 ( 1012) hydrogen bonds : bond 0.01728 ( 25) hydrogen bonds : angle 3.99319 ( 57) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.040 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 3 average time/residue: 0.4339 time to fit residues: 1.3923 Evaluate side-chains 3 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.8730 ------------------------------------------------------------------------------- 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 = 0.4486 r_free = 0.4486 target = 0.057217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.054237 restraints weight = 22229.219| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 3.72 r_work: 0.4300 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5521 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 743 Z= 0.112 Angle : 0.463 4.255 1012 Z= 0.240 Chirality : 0.045 0.144 113 Planarity : 0.005 0.041 136 Dihedral : 4.920 32.902 104 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.04 (0.89), residues: 96 helix: None (None), residues: 0 sheet: 0.10 (0.88), residues: 36 loop : 0.08 (0.85), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.002 ARG M 58 TYR 0.007 0.001 TYR M 79 PHE 0.009 0.002 PHE M 15 HIS 0.002 0.001 HIS M 86 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 743) covalent geometry : angle 0.46304 ( 1012) hydrogen bonds : bond 0.01798 ( 25) hydrogen bonds : angle 3.83518 ( 57) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.043 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.5833 time to fit residues: 1.2505 Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.5730 ------------------------------------------------------------------------------- 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 = 0.4499 r_free = 0.4499 target = 0.057734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.054799 restraints weight = 22512.304| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 3.75 r_work: 0.4305 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5461 moved from start: 0.3778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 743 Z= 0.091 Angle : 0.438 4.148 1012 Z= 0.226 Chirality : 0.045 0.144 113 Planarity : 0.005 0.042 136 Dihedral : 4.761 32.199 104 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.03 (0.88), residues: 96 helix: None (None), residues: 0 sheet: 0.10 (0.88), residues: 36 loop : 0.07 (0.85), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 58 TYR 0.007 0.001 TYR M 79 PHE 0.006 0.001 PHE M 15 HIS 0.001 0.001 HIS M 38 Details of bonding type rmsd covalent geometry : bond 0.00208 ( 743) covalent geometry : angle 0.43790 ( 1012) hydrogen bonds : bond 0.01539 ( 25) hydrogen bonds : angle 3.71173 ( 57) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.024 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.5066 time to fit residues: 1.0796 Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7730 ------------------------------------------------------------------------------- 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 = 0.4462 r_free = 0.4462 target = 0.057784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.054733 restraints weight = 21295.822| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 3.69 r_work: 0.4301 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5532 moved from start: 0.3996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 743 Z= 0.106 Angle : 0.450 4.243 1012 Z= 0.233 Chirality : 0.045 0.142 113 Planarity : 0.005 0.040 136 Dihedral : 4.742 30.765 104 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.07 (0.89), residues: 96 helix: None (None), residues: 0 sheet: 0.19 (0.90), residues: 36 loop : 0.05 (0.85), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 58 TYR 0.007 0.002 TYR M 79 PHE 0.008 0.002 PHE M 15 HIS 0.002 0.001 HIS M 86 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 743) covalent geometry : angle 0.45012 ( 1012) hydrogen bonds : bond 0.01650 ( 25) hydrogen bonds : angle 3.69271 ( 57) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.042 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.5015 time to fit residues: 1.0647 Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4463 r_free = 0.4463 target = 0.057907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.054810 restraints weight = 21238.085| |-----------------------------------------------------------------------------| r_work (start): 0.4350 rms_B_bonded: 3.71 r_work: 0.4294 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5571 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 743 Z= 0.096 Angle : 0.437 4.199 1012 Z= 0.225 Chirality : 0.045 0.144 113 Planarity : 0.005 0.040 136 Dihedral : 4.672 30.133 104 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 9.21 % Favored : 90.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.89), residues: 96 helix: None (None), residues: 0 sheet: 0.26 (0.91), residues: 36 loop : 0.05 (0.85), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 58 TYR 0.007 0.001 TYR M 79 PHE 0.006 0.001 PHE M 15 HIS 0.001 0.001 HIS M 86 Details of bonding type rmsd covalent geometry : bond 0.00217 ( 743) covalent geometry : angle 0.43726 ( 1012) hydrogen bonds : bond 0.01544 ( 25) hydrogen bonds : angle 3.69477 ( 57) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.035 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.3907 time to fit residues: 0.8370 Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7733 ------------------------------------------------------------------------------- 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 = 0.4493 r_free = 0.4493 target = 0.057666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.054588 restraints weight = 22037.214| |-----------------------------------------------------------------------------| r_work (start): 0.4358 rms_B_bonded: 3.78 r_work: 0.4299 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5587 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 743 Z= 0.105 Angle : 0.449 4.269 1012 Z= 0.232 Chirality : 0.045 0.144 113 Planarity : 0.005 0.040 136 Dihedral : 4.699 29.834 104 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.89), residues: 96 helix: None (None), residues: 0 sheet: 0.12 (0.88), residues: 37 loop : 0.08 (0.85), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 58 TYR 0.007 0.001 TYR M 79 PHE 0.008 0.001 PHE M 15 HIS 0.001 0.001 HIS M 86 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 743) covalent geometry : angle 0.44884 ( 1012) hydrogen bonds : bond 0.01643 ( 25) hydrogen bonds : angle 3.75231 ( 57) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.043 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.4603 time to fit residues: 0.9847 Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.057700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.054591 restraints weight = 22089.421| |-----------------------------------------------------------------------------| r_work (start): 0.4347 rms_B_bonded: 3.81 r_work: 0.4290 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5581 moved from start: 0.4336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 743 Z= 0.103 Angle : 0.444 4.253 1012 Z= 0.229 Chirality : 0.045 0.146 113 Planarity : 0.005 0.040 136 Dihedral : 4.705 29.697 104 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.89), residues: 96 helix: None (None), residues: 0 sheet: 0.21 (0.89), residues: 37 loop : 0.10 (0.86), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 58 TYR 0.006 0.001 TYR M 79 PHE 0.007 0.001 PHE M 15 HIS 0.001 0.001 HIS M 86 Details of bonding type rmsd covalent geometry : bond 0.00230 ( 743) covalent geometry : angle 0.44409 ( 1012) hydrogen bonds : bond 0.01593 ( 25) hydrogen bonds : angle 3.78935 ( 57) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 192 Ramachandran restraints generated. 96 Oldfield, 0 Emsley, 96 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.026 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 2 average time/residue: 0.4425 time to fit residues: 0.9490 Evaluate side-chains 2 residues out of total 76 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 9 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7730 ------------------------------------------------------------------------------- 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 = 0.4488 r_free = 0.4488 target = 0.057621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.054425 restraints weight = 22253.336| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 3.89 r_work: 0.4291 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.4291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 0.4465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 743 Z= 0.104 Angle : 0.447 4.261 1012 Z= 0.231 Chirality : 0.045 0.145 113 Planarity : 0.005 0.040 136 Dihedral : 4.721 29.695 104 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.04 % Favored : 98.96 % Rotamer: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 40.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.89), residues: 96 helix: None (None), residues: 0 sheet: 0.19 (0.89), residues: 37 loop : 0.08 (0.85), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG M 58 TYR 0.006 0.001 TYR M 79 PHE 0.008 0.001 PHE M 15 HIS 0.001 0.001 HIS M 86 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 743) covalent geometry : angle 0.44695 ( 1012) hydrogen bonds : bond 0.01632 ( 25) hydrogen bonds : angle 3.75415 ( 57) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1521.37 seconds wall clock time: 27 minutes 17.88 seconds (1637.88 seconds total)