Starting phenix.real_space_refine on Tue Mar 3 10:55:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y14_33556/03_2026/7y14_33556.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y14_33556/03_2026/7y14_33556.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7y14_33556/03_2026/7y14_33556.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y14_33556/03_2026/7y14_33556.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7y14_33556/03_2026/7y14_33556.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y14_33556/03_2026/7y14_33556.map" } resolution = 3.2 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: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 1431 2.51 5 N 342 2.21 5 O 350 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2145 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 2073 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2073 Unusual residues: {'BAL': 1} Classifications: {'peptide': 264, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PRE-BETA-TRANS': 1, 'PTRANS': 10, 'TRANS': 253} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2, 'ASP:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 28 Chain: "R" Number of atoms: 72 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 72 Unusual residues: {'PLM': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 0.59, per 1000 atoms: 0.28 Number of scatterers: 2145 At special positions: 0 Unit cell: (57.375, 68.175, 69.525, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 350 8.00 N 342 7.00 C 1431 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 164 " - pdb=" SG CYS R 175 " distance=2.03 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: 0.20 Conformation dependent library (CDL) restraints added in 49.4 milliseconds 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Skipped Input volumes are d-peptide like pdb=" CB BAL R1001 " Number of C-beta restraints generated: 512 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 81.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'R' and resid 22 through 52 removed outlier: 3.709A pdb=" N LEU R 28 " --> pdb=" O HIS R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 62 through 86 Processing helix chain 'R' and resid 95 through 129 removed outlier: 3.733A pdb=" N VAL R 127 " --> pdb=" O ARG R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 136 Processing helix chain 'R' and resid 140 through 165 Processing helix chain 'R' and resid 172 through 189 Processing helix chain 'R' and resid 189 through 209 Processing helix chain 'R' and resid 216 through 234 Processing helix chain 'R' and resid 234 through 242 removed outlier: 4.188A pdb=" N SER R 238 " --> pdb=" O SER R 234 " (cutoff:3.500A) Processing helix chain 'R' and resid 253 through 277 Proline residue: R 273 - end of helix 171 hydrogen bonds defined for protein. 513 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: 0.31 Time building geometry restraints manager: 0.24 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: 427 1.33 - 1.45: 506 1.45 - 1.57: 1230 1.57 - 1.69: 0 1.69 - 1.81: 33 Bond restraints: 2196 Sorted by residual: bond pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 1.247 1.307 -0.060 2.00e-02 2.50e+03 8.85e+00 bond pdb=" C1 PLM R1002 " pdb=" C2 PLM R1002 " ideal model delta sigma weight residual 1.542 1.569 -0.027 2.00e-02 2.50e+03 1.86e+00 bond pdb=" C1 PLM R1004 " pdb=" C2 PLM R1004 " ideal model delta sigma weight residual 1.542 1.566 -0.024 2.00e-02 2.50e+03 1.45e+00 bond pdb=" CA BAL R1001 " pdb=" C BAL R1001 " ideal model delta sigma weight residual 1.525 1.500 0.025 2.10e-02 2.27e+03 1.40e+00 bond pdb=" C1 PLM R1003 " pdb=" C2 PLM R1003 " ideal model delta sigma weight residual 1.542 1.565 -0.023 2.00e-02 2.50e+03 1.35e+00 ... (remaining 2191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 2836 1.49 - 2.98: 113 2.98 - 4.47: 12 4.47 - 5.96: 5 5.96 - 7.46: 3 Bond angle restraints: 2969 Sorted by residual: angle pdb=" CA BAL R1001 " pdb=" C BAL R1001 " pdb=" OXT BAL R1001 " ideal model delta sigma weight residual 120.80 113.34 7.46 1.70e+00 3.46e-01 1.92e+01 angle pdb=" N BAL R1001 " pdb=" CB BAL R1001 " pdb=" CA BAL R1001 " ideal model delta sigma weight residual 110.40 114.96 -4.56 1.50e+00 4.44e-01 9.23e+00 angle pdb=" N MET R 79 " pdb=" CA MET R 79 " pdb=" CB MET R 79 " ideal model delta sigma weight residual 110.16 113.87 -3.71 1.48e+00 4.57e-01 6.30e+00 angle pdb=" CA TRP R 144 " pdb=" CB TRP R 144 " pdb=" CG TRP R 144 " ideal model delta sigma weight residual 113.60 118.12 -4.52 1.90e+00 2.77e-01 5.65e+00 angle pdb=" C ALA R 143 " pdb=" N TRP R 144 " pdb=" CA TRP R 144 " ideal model delta sigma weight residual 121.14 117.15 3.99 1.75e+00 3.27e-01 5.19e+00 ... (remaining 2964 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.25: 1146 16.25 - 32.51: 131 32.51 - 48.76: 20 48.76 - 65.01: 3 65.01 - 81.27: 1 Dihedral angle restraints: 1301 sinusoidal: 519 harmonic: 782 Sorted by residual: dihedral pdb=" CB GLU R 99 " pdb=" CG GLU R 99 " pdb=" CD GLU R 99 " pdb=" OE1 GLU R 99 " ideal model delta sinusoidal sigma weight residual 0.00 81.27 -81.27 1 3.00e+01 1.11e-03 9.05e+00 dihedral pdb=" CB MET R 180 " pdb=" CG MET R 180 " pdb=" SD MET R 180 " pdb=" CE MET R 180 " ideal model delta sinusoidal sigma weight residual 60.00 110.60 -50.60 3 1.50e+01 4.44e-03 8.92e+00 dihedral pdb=" CA LEU R 228 " pdb=" CB LEU R 228 " pdb=" CG LEU R 228 " pdb=" CD1 LEU R 228 " ideal model delta sinusoidal sigma weight residual 180.00 134.54 45.46 3 1.50e+01 4.44e-03 8.17e+00 ... (remaining 1298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 224 0.031 - 0.063: 95 0.063 - 0.094: 22 0.094 - 0.125: 5 0.125 - 0.157: 5 Chirality restraints: 351 Sorted by residual: chirality pdb=" CA TRP R 144 " pdb=" N TRP R 144 " pdb=" C TRP R 144 " pdb=" CB TRP R 144 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.13e-01 chirality pdb=" CA MET R 79 " pdb=" N MET R 79 " pdb=" C MET R 79 " pdb=" CB MET R 79 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA THR R 191 " pdb=" N THR R 191 " pdb=" C THR R 191 " pdb=" CB THR R 191 " both_signs ideal model delta sigma weight residual False 2.53 2.38 0.15 2.00e-01 2.50e+01 5.62e-01 ... (remaining 348 not shown) Planarity restraints: 348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 144 " -0.020 2.00e-02 2.50e+03 1.58e-02 6.20e+00 pdb=" CG TRP R 144 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TRP R 144 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP R 144 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 144 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 144 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 144 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN R 88 " 0.038 5.00e-02 4.00e+02 5.86e-02 5.49e+00 pdb=" N PRO R 89 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO R 89 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 89 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN R 215 " -0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO R 216 " 0.067 5.00e-02 4.00e+02 pdb=" CA PRO R 216 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 216 " -0.021 5.00e-02 4.00e+02 ... (remaining 345 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 631 2.83 - 3.35: 2146 3.35 - 3.86: 3635 3.86 - 4.38: 3981 4.38 - 4.90: 7063 Nonbonded interactions: 17456 Sorted by model distance: nonbonded pdb=" OD2 ASP R 179 " pdb=" N BAL R1001 " model vdw 2.312 3.120 nonbonded pdb=" OH TYR R 109 " pdb=" O SER R 234 " model vdw 2.332 3.040 nonbonded pdb=" O THR R 191 " pdb=" OG1 THR R 195 " model vdw 2.460 3.040 nonbonded pdb=" O ARG R 55 " pdb=" ND1 HIS R 57 " model vdw 2.461 3.120 nonbonded pdb=" O GLY R 41 " pdb=" ND2 ASN R 45 " model vdw 2.471 3.120 ... (remaining 17451 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=0.00 max=1.00 mean=0.99 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: 1.690 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.200 Find NCS groups from input model: 0.010 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 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 : 0.004 0.060 2197 Z= 0.186 Angle : 0.663 7.456 2971 Z= 0.351 Chirality : 0.039 0.157 351 Planarity : 0.005 0.059 348 Dihedral : 13.603 81.268 786 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 2.46 (0.56), residues: 262 helix: 2.33 (0.37), residues: 207 sheet: None (None), residues: 0 loop : -1.20 (1.01), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 214 TYR 0.012 0.002 TYR R 106 PHE 0.022 0.002 PHE R 75 TRP 0.043 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 2196) covalent geometry : angle 0.66307 ( 2969) SS BOND : bond 0.00544 ( 1) SS BOND : angle 0.99342 ( 2) hydrogen bonds : bond 0.08409 ( 171) hydrogen bonds : angle 5.63905 ( 513) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.058 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0420 time to fit residues: 1.9937 Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 15 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3842 r_free = 0.3842 target = 0.160390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.135765 restraints weight = 2515.151| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.74 r_work: 0.3365 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.0744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2197 Z= 0.142 Angle : 0.565 6.547 2971 Z= 0.288 Chirality : 0.038 0.153 351 Planarity : 0.005 0.056 348 Dihedral : 7.738 59.368 342 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.43 % Allowed : 5.19 % Favored : 94.37 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 2.78 (0.55), residues: 262 helix: 2.48 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.04 (1.05), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 214 TYR 0.016 0.002 TYR R 245 PHE 0.020 0.002 PHE R 75 TRP 0.033 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2196) covalent geometry : angle 0.56474 ( 2969) SS BOND : bond 0.00376 ( 1) SS BOND : angle 0.79311 ( 2) hydrogen bonds : bond 0.03660 ( 171) hydrogen bonds : angle 4.63161 ( 513) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.082 Fit side-chains REVERT: R 101 MET cc_start: 0.6190 (mtp) cc_final: 0.5959 (mtp) REVERT: R 275 ILE cc_start: 0.7932 (tt) cc_final: 0.7724 (pt) outliers start: 1 outliers final: 0 residues processed: 33 average time/residue: 0.0394 time to fit residues: 1.6838 Evaluate side-chains 30 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 19 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3781 r_free = 0.3781 target = 0.154803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129591 restraints weight = 2581.051| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 1.73 r_work: 0.3343 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3212 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2197 Z= 0.130 Angle : 0.530 6.547 2971 Z= 0.270 Chirality : 0.038 0.153 351 Planarity : 0.005 0.053 348 Dihedral : 7.577 58.575 342 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.87 % Allowed : 8.66 % Favored : 90.48 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 3.02 (0.56), residues: 262 helix: 2.67 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.07 (1.06), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 214 TYR 0.016 0.002 TYR R 245 PHE 0.016 0.001 PHE R 75 TRP 0.028 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 2196) covalent geometry : angle 0.52924 ( 2969) SS BOND : bond 0.00420 ( 1) SS BOND : angle 0.86917 ( 2) hydrogen bonds : bond 0.03459 ( 171) hydrogen bonds : angle 4.43784 ( 513) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.088 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 31 average time/residue: 0.0402 time to fit residues: 1.6131 Evaluate side-chains 30 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 11 optimal weight: 0.3980 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 25 optimal weight: 0.0370 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.157083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131342 restraints weight = 2486.746| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 1.74 r_work: 0.3358 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2197 Z= 0.105 Angle : 0.493 6.511 2971 Z= 0.252 Chirality : 0.036 0.154 351 Planarity : 0.005 0.051 348 Dihedral : 7.180 56.956 342 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.43 % Allowed : 13.42 % Favored : 86.15 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 3.31 (0.55), residues: 262 helix: 2.96 (0.36), residues: 209 sheet: None (None), residues: 0 loop : -1.20 (1.01), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 214 TYR 0.017 0.002 TYR R 245 PHE 0.016 0.001 PHE R 75 TRP 0.022 0.001 TRP R 144 HIS 0.001 0.000 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 2196) covalent geometry : angle 0.49319 ( 2969) SS BOND : bond 0.00354 ( 1) SS BOND : angle 0.65701 ( 2) hydrogen bonds : bond 0.03196 ( 171) hydrogen bonds : angle 4.33436 ( 513) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.086 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.0434 time to fit residues: 1.6892 Evaluate side-chains 30 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 22 optimal weight: 0.5980 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3787 r_free = 0.3787 target = 0.155612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.129857 restraints weight = 2523.753| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.72 r_work: 0.3349 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3217 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2197 Z= 0.124 Angle : 0.509 6.431 2971 Z= 0.261 Chirality : 0.037 0.154 351 Planarity : 0.005 0.049 348 Dihedral : 7.376 58.310 342 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.43 % Allowed : 16.45 % Favored : 83.12 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 3.23 (0.55), residues: 262 helix: 2.84 (0.36), residues: 211 sheet: None (None), residues: 0 loop : -1.10 (1.04), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 214 TYR 0.018 0.002 TYR R 245 PHE 0.017 0.001 PHE R 75 TRP 0.023 0.002 TRP R 144 HIS 0.001 0.001 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2196) covalent geometry : angle 0.50854 ( 2969) SS BOND : bond 0.00404 ( 1) SS BOND : angle 0.77515 ( 2) hydrogen bonds : bond 0.03385 ( 171) hydrogen bonds : angle 4.34457 ( 513) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.048 Fit side-chains REVERT: R 101 MET cc_start: 0.6524 (mtp) cc_final: 0.6035 (mmm) outliers start: 1 outliers final: 1 residues processed: 32 average time/residue: 0.0315 time to fit residues: 1.3450 Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 0 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.156071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.130456 restraints weight = 2503.822| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 1.72 r_work: 0.3329 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2197 Z= 0.144 Angle : 0.528 6.522 2971 Z= 0.272 Chirality : 0.038 0.154 351 Planarity : 0.005 0.048 348 Dihedral : 7.454 55.551 342 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.87 % Allowed : 16.45 % Favored : 82.68 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 3.18 (0.55), residues: 262 helix: 2.79 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.04 (1.05), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 214 TYR 0.018 0.002 TYR R 245 PHE 0.020 0.002 PHE R 75 TRP 0.023 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2196) covalent geometry : angle 0.52817 ( 2969) SS BOND : bond 0.00451 ( 1) SS BOND : angle 0.84554 ( 2) hydrogen bonds : bond 0.03494 ( 171) hydrogen bonds : angle 4.36294 ( 513) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.050 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 0.0275 time to fit residues: 1.1955 Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.0060 chunk 21 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.155231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.129751 restraints weight = 2514.515| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 1.71 r_work: 0.3344 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3215 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2197 Z= 0.113 Angle : 0.494 5.509 2971 Z= 0.256 Chirality : 0.036 0.142 351 Planarity : 0.005 0.048 348 Dihedral : 7.267 59.456 342 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.43 % Allowed : 16.45 % Favored : 83.12 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 3.32 (0.55), residues: 262 helix: 2.98 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.30 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 262 TYR 0.019 0.002 TYR R 245 PHE 0.020 0.001 PHE R 75 TRP 0.021 0.001 TRP R 144 HIS 0.001 0.000 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 2196) covalent geometry : angle 0.49429 ( 2969) SS BOND : bond 0.00386 ( 1) SS BOND : angle 0.68101 ( 2) hydrogen bonds : bond 0.03310 ( 171) hydrogen bonds : angle 4.32230 ( 513) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.058 Fit side-chains REVERT: R 101 MET cc_start: 0.6363 (mmm) cc_final: 0.5919 (mmm) outliers start: 1 outliers final: 1 residues processed: 33 average time/residue: 0.0303 time to fit residues: 1.3039 Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 199 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3792 r_free = 0.3792 target = 0.155953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.130090 restraints weight = 2507.144| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.72 r_work: 0.3350 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7509 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2197 Z= 0.126 Angle : 0.510 5.453 2971 Z= 0.266 Chirality : 0.037 0.146 351 Planarity : 0.005 0.047 348 Dihedral : 7.286 57.708 342 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 0.43 % Allowed : 18.18 % Favored : 81.39 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 3.18 (0.55), residues: 262 helix: 2.83 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.25 (1.02), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 214 TYR 0.020 0.002 TYR R 245 PHE 0.022 0.001 PHE R 75 TRP 0.021 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2196) covalent geometry : angle 0.50974 ( 2969) SS BOND : bond 0.00325 ( 1) SS BOND : angle 0.74744 ( 2) hydrogen bonds : bond 0.03375 ( 171) hydrogen bonds : angle 4.26774 ( 513) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.048 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.0285 time to fit residues: 1.1385 Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 199 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 17 optimal weight: 0.4980 chunk 9 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3791 r_free = 0.3791 target = 0.155663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.130058 restraints weight = 2523.660| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 1.71 r_work: 0.3351 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3221 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3221 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2197 Z= 0.121 Angle : 0.507 5.418 2971 Z= 0.264 Chirality : 0.037 0.143 351 Planarity : 0.005 0.047 348 Dihedral : 7.250 58.027 342 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 0.87 % Allowed : 18.18 % Favored : 80.95 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 3.27 (0.55), residues: 262 helix: 2.96 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.37 (0.99), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 214 TYR 0.020 0.002 TYR R 245 PHE 0.022 0.001 PHE R 75 TRP 0.021 0.002 TRP R 144 HIS 0.002 0.001 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 2196) covalent geometry : angle 0.50713 ( 2969) SS BOND : bond 0.00321 ( 1) SS BOND : angle 0.71875 ( 2) hydrogen bonds : bond 0.03397 ( 171) hydrogen bonds : angle 4.28925 ( 513) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.125 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 31 average time/residue: 0.0385 time to fit residues: 1.5777 Evaluate side-chains 32 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 199 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 17 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 19 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- 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 = 0.3766 r_free = 0.3766 target = 0.153493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.127580 restraints weight = 2560.961| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.72 r_work: 0.3326 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3198 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.1331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2197 Z= 0.166 Angle : 0.559 5.524 2971 Z= 0.294 Chirality : 0.039 0.159 351 Planarity : 0.005 0.047 348 Dihedral : 7.545 53.472 342 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 1.30 % Allowed : 18.18 % Favored : 80.52 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 3.05 (0.55), residues: 262 helix: 2.71 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -1.18 (1.05), residues: 51 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 214 TYR 0.021 0.002 TYR R 245 PHE 0.026 0.002 PHE R 75 TRP 0.023 0.002 TRP R 144 HIS 0.003 0.001 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 2196) covalent geometry : angle 0.55866 ( 2969) SS BOND : bond 0.00412 ( 1) SS BOND : angle 0.96444 ( 2) hydrogen bonds : bond 0.03755 ( 171) hydrogen bonds : angle 4.36735 ( 513) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 524 Ramachandran restraints generated. 262 Oldfield, 0 Emsley, 262 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.099 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 32 average time/residue: 0.0388 time to fit residues: 1.5936 Evaluate side-chains 33 residues out of total 242 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 114 SER Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 199 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 26 random chunks: chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 6 optimal weight: 0.0470 chunk 12 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.155526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.129665 restraints weight = 2556.066| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 1.73 r_work: 0.3350 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.1343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2197 Z= 0.114 Angle : 0.519 6.824 2971 Z= 0.269 Chirality : 0.037 0.140 351 Planarity : 0.005 0.047 348 Dihedral : 7.232 58.316 342 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.30 % Allowed : 18.18 % Favored : 80.52 % Cbeta Deviations : 0.39 % 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 are not related in a simple way. whole: 3.26 (0.55), residues: 262 helix: 2.95 (0.35), residues: 209 sheet: None (None), residues: 0 loop : -1.33 (1.00), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 214 TYR 0.019 0.002 TYR R 245 PHE 0.022 0.001 PHE R 75 TRP 0.021 0.001 TRP R 144 HIS 0.001 0.000 HIS R 98 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 2196) covalent geometry : angle 0.51863 ( 2969) SS BOND : bond 0.00310 ( 1) SS BOND : angle 0.71634 ( 2) hydrogen bonds : bond 0.03394 ( 171) hydrogen bonds : angle 4.29763 ( 513) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 764.13 seconds wall clock time: 13 minutes 48.56 seconds (828.56 seconds total)