Starting phenix.real_space_refine on Fri Aug 22 12:38:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hvc_52431/08_2025/9hvc_52431.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hvc_52431/08_2025/9hvc_52431.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hvc_52431/08_2025/9hvc_52431.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hvc_52431/08_2025/9hvc_52431.map" model { file = "/net/cci-nas-00/data/ceres_data/9hvc_52431/08_2025/9hvc_52431.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hvc_52431/08_2025/9hvc_52431.cif" } resolution = 2.24 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= 0.003 sd= 0.055 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 P 1 5.49 5 S 6 5.16 5 C 363 2.51 5 N 75 2.21 5 O 133 1.98 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-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 578 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 498 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "A" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 80 Unusual residues: {'LHG': 1} Classifications: {'undetermined': 1, 'water': 31} Link IDs: {None: 31} Time building chain proxies: 0.27, per 1000 atoms: 0.47 Number of scatterers: 578 At special positions: 0 Unit cell: (38.76, 53.04, 58.14, 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 6 16.00 P 1 15.00 O 133 8.00 N 75 7.00 C 363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " GLY A 1 " - " ASP A 69 " Time building additional restraints: 0.07 Conformation dependent library (CDL) restraints added in 137.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 120 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.02 Creating SS restraints... Processing helix chain 'A' and resid 7 through 20 removed outlier: 4.104A pdb=" N THR A 19 " --> pdb=" O SER A 15 " (cutoff:3.500A) Processing helix chain 'A' and resid 20 through 38 Processing helix chain 'A' and resid 44 through 59 Processing helix chain 'A' and resid 59 through 68 42 hydrogen bonds defined for protein. 126 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: 0.04 Time building geometry restraints manager: 0.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 100 1.33 - 1.45: 121 1.45 - 1.57: 321 1.57 - 1.69: 2 1.69 - 1.80: 11 Bond restraints: 555 Sorted by residual: bond pdb=" C23 LHG A 101 " pdb=" O8 LHG A 101 " ideal model delta sigma weight residual 1.328 1.366 -0.038 2.00e-02 2.50e+03 3.65e+00 bond pdb=" C7 LHG A 101 " pdb=" O7 LHG A 101 " ideal model delta sigma weight residual 1.329 1.362 -0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C7 LHG A 101 " pdb=" C8 LHG A 101 " ideal model delta sigma weight residual 1.507 1.476 0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" C20 LHG A 101 " pdb=" C21 LHG A 101 " ideal model delta sigma weight residual 1.527 1.497 0.030 2.00e-02 2.50e+03 2.32e+00 bond pdb=" C36 LHG A 101 " pdb=" C37 LHG A 101 " ideal model delta sigma weight residual 1.526 1.497 0.029 2.00e-02 2.50e+03 2.09e+00 ... (remaining 550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 702 2.49 - 4.99: 16 4.99 - 7.48: 9 7.48 - 9.97: 6 9.97 - 12.46: 5 Bond angle restraints: 738 Sorted by residual: angle pdb=" O4 LHG A 101 " pdb=" P LHG A 101 " pdb=" O5 LHG A 101 " ideal model delta sigma weight residual 120.69 133.15 -12.46 3.00e+00 1.11e-01 1.73e+01 angle pdb=" C2 LHG A 101 " pdb=" C3 LHG A 101 " pdb=" O3 LHG A 101 " ideal model delta sigma weight residual 111.30 99.73 11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C11 LHG A 101 " pdb=" C10 LHG A 101 " pdb=" C9 LHG A 101 " ideal model delta sigma weight residual 112.80 101.96 10.84 3.00e+00 1.11e-01 1.31e+01 angle pdb=" C18 LHG A 101 " pdb=" C19 LHG A 101 " pdb=" C20 LHG A 101 " ideal model delta sigma weight residual 113.04 102.58 10.46 3.00e+00 1.11e-01 1.22e+01 angle pdb=" C16 LHG A 101 " pdb=" C17 LHG A 101 " pdb=" C18 LHG A 101 " ideal model delta sigma weight residual 113.58 103.50 10.08 3.00e+00 1.11e-01 1.13e+01 ... (remaining 733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.39: 262 14.39 - 28.77: 48 28.77 - 43.16: 18 43.16 - 57.55: 10 57.55 - 71.93: 4 Dihedral angle restraints: 342 sinusoidal: 151 harmonic: 191 Sorted by residual: dihedral pdb=" CA GLY A 1 " pdb=" N GLY A 1 " pdb=" C ASP A 69 " pdb=" CA ASP A 69 " ideal model delta harmonic sigma weight residual 180.00 155.11 24.89 0 5.00e+00 4.00e-02 2.48e+01 dihedral pdb=" CA ASN A 43 " pdb=" CB ASN A 43 " pdb=" CG ASN A 43 " pdb=" OD1 ASN A 43 " ideal model delta sinusoidal sigma weight residual -90.00 -161.93 71.93 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CB LYS A 41 " pdb=" CG LYS A 41 " pdb=" CD LYS A 41 " pdb=" CE LYS A 41 " ideal model delta sinusoidal sigma weight residual 60.00 118.06 -58.06 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 339 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.019: 37 0.019 - 0.037: 22 0.037 - 0.055: 4 0.055 - 0.073: 14 0.073 - 0.091: 4 Chirality restraints: 81 Sorted by residual: chirality pdb=" CA PRO A 22 " pdb=" N PRO A 22 " pdb=" C PRO A 22 " pdb=" CB PRO A 22 " both_signs ideal model delta sigma weight residual False 2.72 2.63 0.09 2.00e-01 2.50e+01 2.08e-01 chirality pdb=" C5 LHG A 101 " pdb=" C4 LHG A 101 " pdb=" C6 LHG A 101 " pdb=" O7 LHG A 101 " both_signs ideal model delta sigma weight residual False -2.53 -2.62 0.09 2.00e-01 2.50e+01 2.01e-01 chirality pdb=" CA ASN A 43 " pdb=" N ASN A 43 " pdb=" C ASN A 43 " pdb=" CB ASN A 43 " both_signs ideal model delta sigma weight residual False 2.51 2.59 -0.08 2.00e-01 2.50e+01 1.64e-01 ... (remaining 78 not shown) Planarity restraints: 88 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C7 LHG A 101 " -0.066 2.00e-02 2.50e+03 3.82e-02 1.46e+01 pdb=" C8 LHG A 101 " 0.019 2.00e-02 2.50e+03 pdb=" O7 LHG A 101 " 0.020 2.00e-02 2.50e+03 pdb=" O9 LHG A 101 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 43 " -0.007 2.00e-02 2.50e+03 1.51e-02 2.28e+00 pdb=" CG ASN A 43 " 0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN A 43 " -0.010 2.00e-02 2.50e+03 pdb=" ND2 ASN A 43 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 LHG A 101 " 0.025 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C24 LHG A 101 " -0.008 2.00e-02 2.50e+03 pdb=" O10 LHG A 101 " -0.009 2.00e-02 2.50e+03 pdb=" O8 LHG A 101 " -0.008 2.00e-02 2.50e+03 ... (remaining 85 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 21 2.73 - 3.27: 581 3.27 - 3.81: 936 3.81 - 4.36: 1069 4.36 - 4.90: 1652 Nonbonded interactions: 4259 Sorted by model distance: nonbonded pdb=" O2 LHG A 101 " pdb=" O3 LHG A 101 " model vdw 2.184 2.432 nonbonded pdb=" O ASP A 69 " pdb=" O HOH A 201 " model vdw 2.269 3.040 nonbonded pdb=" O HOH A 206 " pdb=" O HOH A 218 " model vdw 2.283 3.040 nonbonded pdb=" O6 LHG A 101 " pdb=" O7 LHG A 101 " model vdw 2.307 2.432 nonbonded pdb=" O HOH A 230 " pdb=" O HOH A 231 " model vdw 2.309 3.040 ... (remaining 4254 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.850 Find NCS groups from input model: 0.000 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:5.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5732 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 : 0.006 0.038 556 Z= 0.285 Angle : 1.608 12.463 741 Z= 0.599 Chirality : 0.037 0.091 81 Planarity : 0.005 0.038 87 Dihedral : 19.496 71.933 219 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 2.75 (0.99), residues: 67 helix: 2.47 (0.64), residues: 57 sheet: None (None), residues: 0 loop : -2.33 (1.71), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR A 13 PHE 0.005 0.001 PHE A 37 TRP 0.002 0.001 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00583 ( 555) covalent geometry : angle 1.54436 ( 738) hydrogen bonds : bond 0.15986 ( 42) hydrogen bonds : angle 5.38301 ( 126) link_TRANS : bond 0.00093 ( 1) link_TRANS : angle 7.19268 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.012 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.3595 time to fit residues: 4.3644 Evaluate side-chains 10 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.0000 chunk 5 optimal weight: 3.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- 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 = 0.3661 r_free = 0.3661 target = 0.136445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.123222 restraints weight = 612.438| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.31 r_work: 0.3392 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3309 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.8906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 556 Z= 0.146 Angle : 0.579 4.445 741 Z= 0.259 Chirality : 0.036 0.093 81 Planarity : 0.004 0.025 87 Dihedral : 16.743 57.321 115 Min Nonbonded Distance : 2.683 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 15.69 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.15 (0.94), residues: 67 helix: 2.73 (0.60), residues: 57 sheet: None (None), residues: 0 loop : -2.06 (1.78), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.010 0.002 TYR A 13 PHE 0.004 0.001 PHE A 37 TRP 0.003 0.001 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 555) covalent geometry : angle 0.57941 ( 738) hydrogen bonds : bond 0.02599 ( 42) hydrogen bonds : angle 3.99011 ( 126) link_TRANS : bond 0.00069 ( 1) link_TRANS : angle 0.57431 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 11 time to evaluate : 0.025 Fit side-chains REVERT: A 53 MET cc_start: 0.8402 (OUTLIER) cc_final: 0.7999 (tpt) outliers start: 2 outliers final: 0 residues processed: 12 average time/residue: 0.6870 time to fit residues: 8.3159 Evaluate side-chains 10 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 9 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 overall best weight: 0.9650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.123991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.110738 restraints weight = 558.638| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.27 r_work: 0.3228 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.9975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 556 Z= 0.108 Angle : 0.367 4.531 741 Z= 0.190 Chirality : 0.035 0.087 81 Planarity : 0.003 0.025 87 Dihedral : 13.299 49.959 115 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.96 % Allowed : 15.69 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (1.01), residues: 67 helix: 3.15 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.07 (1.82), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.002 TYR A 13 PHE 0.007 0.001 PHE A 7 TRP 0.002 0.001 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 555) covalent geometry : angle 0.36635 ( 738) hydrogen bonds : bond 0.03483 ( 42) hydrogen bonds : angle 4.00894 ( 126) link_TRANS : bond 0.00022 ( 1) link_TRANS : angle 0.47717 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.023 Fit side-chains REVERT: A 53 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8086 (tpt) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 0.6831 time to fit residues: 8.2740 Evaluate side-chains 13 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7647 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.125280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.112305 restraints weight = 581.491| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.27 r_work: 0.3253 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 1.0353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 556 Z= 0.083 Angle : 0.331 4.587 741 Z= 0.168 Chirality : 0.033 0.090 81 Planarity : 0.003 0.023 87 Dihedral : 12.432 52.051 115 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 4.02 (1.00), residues: 67 helix: 3.35 (0.64), residues: 57 sheet: None (None), residues: 0 loop : -2.05 (1.72), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR A 13 PHE 0.005 0.001 PHE A 7 TRP 0.002 0.001 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00159 ( 555) covalent geometry : angle 0.33158 ( 738) hydrogen bonds : bond 0.02727 ( 42) hydrogen bonds : angle 3.75297 ( 126) link_TRANS : bond 0.00052 ( 1) link_TRANS : angle 0.25603 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.044 Fit side-chains REVERT: A 53 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8149 (tpt) outliers start: 1 outliers final: 0 residues processed: 12 average time/residue: 0.7020 time to fit residues: 8.4914 Evaluate side-chains 12 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 11 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.123124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.110334 restraints weight = 563.824| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 1.25 r_work: 0.3232 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 1.0483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 556 Z= 0.088 Angle : 0.332 4.687 741 Z= 0.172 Chirality : 0.034 0.089 81 Planarity : 0.003 0.022 87 Dihedral : 12.625 50.385 115 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 4.18 (1.01), residues: 67 helix: 3.48 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.09 (1.67), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 13 PHE 0.004 0.001 PHE A 7 TRP 0.001 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00171 ( 555) covalent geometry : angle 0.33145 ( 738) hydrogen bonds : bond 0.02827 ( 42) hydrogen bonds : angle 3.79260 ( 126) link_TRANS : bond 0.00030 ( 1) link_TRANS : angle 0.36206 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.023 Fit side-chains REVERT: A 53 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8174 (tpt) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.5877 time to fit residues: 8.2996 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.122288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109490 restraints weight = 602.445| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.32 r_work: 0.3208 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 3.00 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 1.0700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 556 Z= 0.089 Angle : 0.335 4.684 741 Z= 0.171 Chirality : 0.033 0.089 81 Planarity : 0.003 0.022 87 Dihedral : 12.616 50.331 115 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 11.76 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 4.20 (1.00), residues: 67 helix: 3.49 (0.64), residues: 57 sheet: None (None), residues: 0 loop : -2.08 (1.64), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR A 13 PHE 0.005 0.001 PHE A 7 TRP 0.001 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00172 ( 555) covalent geometry : angle 0.33484 ( 738) hydrogen bonds : bond 0.02921 ( 42) hydrogen bonds : angle 3.81669 ( 126) link_TRANS : bond 0.00030 ( 1) link_TRANS : angle 0.34726 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.021 Fit side-chains REVERT: A 53 MET cc_start: 0.8647 (OUTLIER) cc_final: 0.8170 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.6565 time to fit residues: 8.6019 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 overall best weight: 0.7650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.123251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.110798 restraints weight = 605.345| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.28 r_work: 0.3218 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 1.0637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.011 556 Z= 0.085 Angle : 0.333 4.720 741 Z= 0.172 Chirality : 0.034 0.090 81 Planarity : 0.003 0.022 87 Dihedral : 12.493 51.840 115 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 11.76 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 4.40 (1.01), residues: 67 helix: 3.64 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.11 (1.59), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR A 13 PHE 0.003 0.001 PHE A 7 TRP 0.001 0.000 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00164 ( 555) covalent geometry : angle 0.33293 ( 738) hydrogen bonds : bond 0.02733 ( 42) hydrogen bonds : angle 3.79014 ( 126) link_TRANS : bond 0.00054 ( 1) link_TRANS : angle 0.20001 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 15 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 14 time to evaluate : 0.021 Fit side-chains REVERT: A 53 MET cc_start: 0.8577 (OUTLIER) cc_final: 0.8091 (tpt) outliers start: 1 outliers final: 0 residues processed: 14 average time/residue: 0.6003 time to fit residues: 8.4770 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.3323 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.119870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.107660 restraints weight = 599.659| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.28 r_work: 0.3174 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3075 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 1.0678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 556 Z= 0.109 Angle : 0.358 4.718 741 Z= 0.182 Chirality : 0.034 0.088 81 Planarity : 0.003 0.022 87 Dihedral : 13.079 51.963 115 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 4.21 (1.02), residues: 67 helix: 3.50 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -2.11 (1.59), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR A 13 PHE 0.005 0.001 PHE A 7 TRP 0.002 0.001 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 555) covalent geometry : angle 0.35859 ( 738) hydrogen bonds : bond 0.03273 ( 42) hydrogen bonds : angle 3.98390 ( 126) link_TRANS : bond 0.00124 ( 1) link_TRANS : angle 0.16985 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.027 Fit side-chains REVERT: A 53 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.8028 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.7210 time to fit residues: 9.4549 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 overall best weight: 1.2987 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.120193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.108478 restraints weight = 593.748| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 1.26 r_work: 0.3187 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 1.0707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 556 Z= 0.109 Angle : 0.363 4.761 741 Z= 0.188 Chirality : 0.035 0.091 81 Planarity : 0.003 0.021 87 Dihedral : 13.161 56.632 115 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 4.27 (1.02), residues: 67 helix: 3.55 (0.66), residues: 57 sheet: None (None), residues: 0 loop : -2.16 (1.57), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR A 13 PHE 0.004 0.001 PHE A 7 TRP 0.002 0.001 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00222 ( 555) covalent geometry : angle 0.36345 ( 738) hydrogen bonds : bond 0.03135 ( 42) hydrogen bonds : angle 3.94207 ( 126) link_TRANS : bond 0.00120 ( 1) link_TRANS : angle 0.17572 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.023 Fit side-chains REVERT: A 53 MET cc_start: 0.8573 (OUTLIER) cc_final: 0.8037 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.6496 time to fit residues: 8.5186 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 overall best weight: 2.6657 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.116922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.104856 restraints weight = 589.587| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 1.27 r_work: 0.3141 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 1.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 556 Z= 0.178 Angle : 0.429 4.777 741 Z= 0.216 Chirality : 0.037 0.093 81 Planarity : 0.003 0.022 87 Dihedral : 14.328 56.653 115 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 11.76 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 3.80 (1.01), residues: 67 helix: 3.20 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.09 (1.63), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.012 0.003 TYR A 13 PHE 0.008 0.002 PHE A 37 TRP 0.003 0.001 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00389 ( 555) covalent geometry : angle 0.42960 ( 738) hydrogen bonds : bond 0.04006 ( 42) hydrogen bonds : angle 4.16573 ( 126) link_TRANS : bond 0.00320 ( 1) link_TRANS : angle 0.15165 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 134 Ramachandran restraints generated. 67 Oldfield, 0 Emsley, 67 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.023 Fit side-chains REVERT: A 53 MET cc_start: 0.8571 (OUTLIER) cc_final: 0.8006 (tpt) outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.6507 time to fit residues: 8.5311 Evaluate side-chains 14 residues out of total 51 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 13 time to evaluate : 0.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 6 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.118273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.106270 restraints weight = 590.422| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.27 r_work: 0.3161 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 1.0734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 556 Z= 0.144 Angle : 0.396 4.731 741 Z= 0.201 Chirality : 0.036 0.091 81 Planarity : 0.003 0.023 87 Dihedral : 13.860 50.293 115 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 1.96 % Allowed : 13.73 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 aren not related in a simple way. whole: 3.79 (1.01), residues: 67 helix: 3.18 (0.65), residues: 57 sheet: None (None), residues: 0 loop : -2.00 (1.63), residues: 10 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR A 13 PHE 0.007 0.002 PHE A 37 TRP 0.002 0.001 TRP A 11 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 555) covalent geometry : angle 0.39708 ( 738) hydrogen bonds : bond 0.03701 ( 42) hydrogen bonds : angle 4.08231 ( 126) link_TRANS : bond 0.00212 ( 1) link_TRANS : angle 0.12209 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 497.53 seconds wall clock time: 10 minutes 39.57 seconds (639.57 seconds total)