Starting phenix.real_space_refine on Wed Sep 17 02:58:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zf7_60052/09_2025/8zf7_60052_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zf7_60052/09_2025/8zf7_60052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zf7_60052/09_2025/8zf7_60052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zf7_60052/09_2025/8zf7_60052.map" model { file = "/net/cci-nas-00/data/ceres_data/8zf7_60052/09_2025/8zf7_60052_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zf7_60052/09_2025/8zf7_60052_neut.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.015 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 13 5.16 5 C 1356 2.51 5 N 359 2.21 5 O 348 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2076 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2076 Classifications: {'peptide': 288} Incomplete info: {'truncation_to_alanine': 39} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 269} Chain breaks: 1 Unresolved non-hydrogen bonds: 137 Unresolved non-hydrogen angles: 173 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 8, 'ASP:plan': 3, 'ASN:plan1': 2, 'GLN:plan1': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 71 Time building chain proxies: 0.48, per 1000 atoms: 0.23 Number of scatterers: 2076 At special positions: 0 Unit cell: (58.3, 61.48, 73.14, 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 13 16.00 O 348 8.00 N 359 7.00 C 1356 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 90 " - pdb=" SG CYS R 168 " 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: 0.09 Conformation dependent library (CDL) restraints added in 47.3 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 528 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 1 sheets defined 82.3% alpha, 0.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'R' and resid 18 through 47 removed outlier: 4.559A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) Proline residue: R 33 - end of helix Processing helix chain 'R' and resid 51 through 79 removed outlier: 4.125A pdb=" N TYR R 55 " --> pdb=" O GLU R 51 " (cutoff:3.500A) Proline residue: R 71 - end of helix Processing helix chain 'R' and resid 86 through 121 removed outlier: 4.008A pdb=" N TYR R 102 " --> pdb=" O TYR R 98 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA R 105 " --> pdb=" O LEU R 101 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 125 removed outlier: 3.915A pdb=" N PHE R 125 " --> pdb=" O PRO R 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 122 through 125' Processing helix chain 'R' and resid 129 through 150 removed outlier: 3.774A pdb=" N SER R 133 " --> pdb=" O ARG R 129 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 155 removed outlier: 3.648A pdb=" N GLY R 155 " --> pdb=" O PRO R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 191 removed outlier: 3.708A pdb=" N ALA R 182 " --> pdb=" O GLY R 178 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 209 removed outlier: 3.588A pdb=" N LEU R 209 " --> pdb=" O LEU R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 216 through 253 removed outlier: 3.538A pdb=" N VAL R 223 " --> pdb=" O GLU R 219 " (cutoff:3.500A) Proline residue: R 231 - end of helix Proline residue: R 240 - end of helix Processing helix chain 'R' and resid 265 through 284 Proline residue: R 273 - end of helix Processing helix chain 'R' and resid 287 through 295 Processing helix chain 'R' and resid 297 through 308 Processing sheet with id=AA1, first strand: chain 'R' and resid 158 through 159 168 hydrogen bonds defined for protein. 498 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.16 Time building geometry restraints manager: 0.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 659 1.34 - 1.46: 533 1.46 - 1.58: 927 1.58 - 1.70: 0 1.70 - 1.82: 16 Bond restraints: 2135 Sorted by residual: bond pdb=" N ASP R 81 " pdb=" CA ASP R 81 " ideal model delta sigma weight residual 1.456 1.498 -0.042 1.23e-02 6.61e+03 1.16e+01 bond pdb=" N GLY R 155 " pdb=" CA GLY R 155 " ideal model delta sigma weight residual 1.443 1.459 -0.016 8.60e-03 1.35e+04 3.61e+00 bond pdb=" CA ASP R 81 " pdb=" CB ASP R 81 " ideal model delta sigma weight residual 1.541 1.563 -0.022 1.20e-02 6.94e+03 3.38e+00 bond pdb=" N ARG R 79 " pdb=" CA ARG R 79 " ideal model delta sigma weight residual 1.458 1.438 0.020 1.12e-02 7.97e+03 3.07e+00 bond pdb=" C GLY R 86 " pdb=" N PRO R 87 " ideal model delta sigma weight residual 1.336 1.317 0.019 1.20e-02 6.94e+03 2.60e+00 ... (remaining 2130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 2769 1.68 - 3.37: 123 3.37 - 5.05: 18 5.05 - 6.73: 14 6.73 - 8.41: 3 Bond angle restraints: 2927 Sorted by residual: angle pdb=" N ASP R 81 " pdb=" CA ASP R 81 " pdb=" C ASP R 81 " ideal model delta sigma weight residual 113.28 121.69 -8.41 1.57e+00 4.06e-01 2.87e+01 angle pdb=" N ARG R 80 " pdb=" CA ARG R 80 " pdb=" C ARG R 80 " ideal model delta sigma weight residual 111.39 117.21 -5.82 1.38e+00 5.25e-01 1.78e+01 angle pdb=" N PRO R 71 " pdb=" CA PRO R 71 " pdb=" C PRO R 71 " ideal model delta sigma weight residual 110.70 115.30 -4.60 1.22e+00 6.72e-01 1.42e+01 angle pdb=" N ARG R 79 " pdb=" CA ARG R 79 " pdb=" C ARG R 79 " ideal model delta sigma weight residual 112.97 109.47 3.50 1.06e+00 8.90e-01 1.09e+01 angle pdb=" N VAL R 82 " pdb=" CA VAL R 82 " pdb=" C VAL R 82 " ideal model delta sigma weight residual 109.55 113.35 -3.80 1.38e+00 5.25e-01 7.58e+00 ... (remaining 2922 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.13: 1093 14.13 - 28.26: 109 28.26 - 42.40: 26 42.40 - 56.53: 4 56.53 - 70.66: 2 Dihedral angle restraints: 1234 sinusoidal: 404 harmonic: 830 Sorted by residual: dihedral pdb=" N ASP R 81 " pdb=" C ASP R 81 " pdb=" CA ASP R 81 " pdb=" CB ASP R 81 " ideal model delta harmonic sigma weight residual 122.80 134.58 -11.78 0 2.50e+00 1.60e-01 2.22e+01 dihedral pdb=" CA LEU R 192 " pdb=" C LEU R 192 " pdb=" N LEU R 193 " pdb=" CA LEU R 193 " ideal model delta harmonic sigma weight residual 180.00 158.57 21.43 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA SER R 175 " pdb=" C SER R 175 " pdb=" N GLY R 176 " pdb=" CA GLY R 176 " ideal model delta harmonic sigma weight residual 180.00 159.36 20.64 0 5.00e+00 4.00e-02 1.70e+01 ... (remaining 1231 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 295 0.084 - 0.168: 34 0.168 - 0.252: 1 0.252 - 0.336: 1 0.336 - 0.419: 1 Chirality restraints: 332 Sorted by residual: chirality pdb=" CA ASP R 81 " pdb=" N ASP R 81 " pdb=" C ASP R 81 " pdb=" CB ASP R 81 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.40e+00 chirality pdb=" CA ARG R 80 " pdb=" N ARG R 80 " pdb=" C ARG R 80 " pdb=" CB ARG R 80 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CA HIS R 276 " pdb=" N HIS R 276 " pdb=" C HIS R 276 " pdb=" CB HIS R 276 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.10e-01 ... (remaining 329 not shown) Planarity restraints: 373 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 230 " -0.061 5.00e-02 4.00e+02 9.11e-02 1.33e+01 pdb=" N PRO R 231 " 0.157 5.00e-02 4.00e+02 pdb=" CA PRO R 231 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO R 231 " -0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 86 " -0.032 5.00e-02 4.00e+02 4.76e-02 3.63e+00 pdb=" N PRO R 87 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO R 87 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO R 87 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY R 239 " 0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO R 240 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 240 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 240 " 0.022 5.00e-02 4.00e+02 ... (remaining 370 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 612 2.82 - 3.34: 2092 3.34 - 3.86: 3401 3.86 - 4.38: 3595 4.38 - 4.90: 6331 Nonbonded interactions: 16031 Sorted by model distance: nonbonded pdb=" O GLY R 31 " pdb=" N ASN R 35 " model vdw 2.300 3.120 nonbonded pdb=" OE1 GLU R 170 " pdb=" OH TYR R 172 " model vdw 2.349 3.040 nonbonded pdb=" O TYR R 275 " pdb=" OG SER R 278 " model vdw 2.471 3.040 nonbonded pdb=" NH1 ARG R 91 " pdb=" O LEU R 153 " model vdw 2.496 3.120 nonbonded pdb=" O VAL R 18 " pdb=" OG SER R 22 " model vdw 2.557 3.040 ... (remaining 16026 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: 1.470 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: 0.020 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.420 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:0.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 4.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 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 : 0.007 0.053 2136 Z= 0.297 Angle : 0.897 8.413 2929 Z= 0.486 Chirality : 0.057 0.419 332 Planarity : 0.008 0.091 373 Dihedral : 12.636 70.659 703 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.54 % Allowed : 1.09 % Favored : 98.37 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 11.11 % 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: -0.35 (0.50), residues: 284 helix: 0.77 (0.36), residues: 218 sheet: None (None), residues: 0 loop : -3.66 (0.57), residues: 66 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 248 TYR 0.016 0.002 TYR R 275 PHE 0.015 0.002 PHE R 107 TRP 0.014 0.002 TRP R 83 HIS 0.009 0.003 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00676 ( 2135) covalent geometry : angle 0.89611 ( 2927) SS BOND : bond 0.00081 ( 1) SS BOND : angle 1.86924 ( 2) hydrogen bonds : bond 0.13152 ( 168) hydrogen bonds : angle 5.52526 ( 498) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.042 Fit side-chains REVERT: R 66 LEU cc_start: 0.8090 (tp) cc_final: 0.7885 (tt) REVERT: R 236 LEU cc_start: 0.7697 (tp) cc_final: 0.7477 (tp) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.0421 time to fit residues: 1.6720 Evaluate side-chains 31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.3980 chunk 12 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.2980 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 26 optimal weight: 0.6980 chunk 9 optimal weight: 0.0980 overall best weight: 0.2780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.123310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112804 restraints weight = 3275.364| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.71 r_work: 0.3406 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 2136 Z= 0.175 Angle : 0.713 6.577 2929 Z= 0.363 Chirality : 0.043 0.138 332 Planarity : 0.006 0.061 373 Dihedral : 4.817 21.088 318 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 0.54 % Allowed : 10.87 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.51 (0.51), residues: 284 helix: 1.36 (0.36), residues: 216 sheet: None (None), residues: 0 loop : -3.15 (0.62), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 248 TYR 0.013 0.001 TYR R 275 PHE 0.012 0.001 PHE R 107 TRP 0.005 0.001 TRP R 83 HIS 0.003 0.001 HIS R 159 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 2135) covalent geometry : angle 0.71149 ( 2927) SS BOND : bond 0.00213 ( 1) SS BOND : angle 1.65715 ( 2) hydrogen bonds : bond 0.04349 ( 168) hydrogen bonds : angle 4.62682 ( 498) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.040 Fit side-chains REVERT: R 22 SER cc_start: 0.8664 (m) cc_final: 0.8400 (p) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.0433 time to fit residues: 1.5167 Evaluate side-chains 31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 16 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 23 optimal weight: 0.2980 chunk 19 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 1 optimal weight: 0.8980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 165 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 276 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.122921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.112612 restraints weight = 3316.018| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 1.70 r_work: 0.3404 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 2136 Z= 0.179 Angle : 0.690 6.606 2929 Z= 0.352 Chirality : 0.042 0.128 332 Planarity : 0.006 0.049 373 Dihedral : 4.615 21.031 318 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.63 % Allowed : 14.67 % Favored : 83.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 0.89 (0.52), residues: 284 helix: 1.66 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -3.10 (0.62), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 222 TYR 0.012 0.001 TYR R 275 PHE 0.013 0.001 PHE R 107 TRP 0.007 0.002 TRP R 83 HIS 0.002 0.001 HIS R 159 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 2135) covalent geometry : angle 0.68991 ( 2927) SS BOND : bond 0.00126 ( 1) SS BOND : angle 1.23915 ( 2) hydrogen bonds : bond 0.04205 ( 168) hydrogen bonds : angle 4.47842 ( 498) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.077 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 33 average time/residue: 0.0916 time to fit residues: 3.4481 Evaluate side-chains 29 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 0.0010 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 chunk 7 optimal weight: 0.4980 chunk 14 optimal weight: 0.0270 chunk 17 optimal weight: 0.0970 chunk 6 optimal weight: 0.0870 overall best weight: 0.0620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 165 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.129732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.119096 restraints weight = 3279.291| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.76 r_work: 0.3504 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3385 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2136 Z= 0.129 Angle : 0.656 7.991 2929 Z= 0.323 Chirality : 0.039 0.131 332 Planarity : 0.005 0.050 373 Dihedral : 4.197 21.487 318 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.54 % Allowed : 17.39 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.46 (0.52), residues: 284 helix: 2.15 (0.36), residues: 216 sheet: None (None), residues: 0 loop : -3.19 (0.60), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 225 TYR 0.009 0.001 TYR R 76 PHE 0.009 0.001 PHE R 97 TRP 0.006 0.001 TRP R 83 HIS 0.002 0.001 HIS R 159 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 2135) covalent geometry : angle 0.65574 ( 2927) SS BOND : bond 0.00128 ( 1) SS BOND : angle 0.99482 ( 2) hydrogen bonds : bond 0.03109 ( 168) hydrogen bonds : angle 4.01803 ( 498) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.078 Fit side-chains REVERT: R 78 LEU cc_start: 0.6760 (mt) cc_final: 0.6430 (tp) outliers start: 1 outliers final: 0 residues processed: 34 average time/residue: 0.0741 time to fit residues: 2.9496 Evaluate side-chains 30 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.0970 chunk 7 optimal weight: 0.4980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.0980 chunk 27 optimal weight: 0.0870 chunk 18 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 0 optimal weight: 0.5980 chunk 9 optimal weight: 0.0980 chunk 14 optimal weight: 0.7980 overall best weight: 0.1356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 58 ASN R 159 HIS R 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117211 restraints weight = 3293.855| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 1.77 r_work: 0.3472 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2136 Z= 0.135 Angle : 0.672 7.466 2929 Z= 0.330 Chirality : 0.040 0.128 332 Planarity : 0.005 0.049 373 Dihedral : 4.160 21.547 318 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.09 % Allowed : 16.30 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.59 (0.52), residues: 284 helix: 2.15 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -3.02 (0.65), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 222 TYR 0.011 0.001 TYR R 76 PHE 0.009 0.001 PHE R 107 TRP 0.005 0.001 TRP R 43 HIS 0.002 0.001 HIS R 159 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 2135) covalent geometry : angle 0.67207 ( 2927) SS BOND : bond 0.00146 ( 1) SS BOND : angle 0.87730 ( 2) hydrogen bonds : bond 0.03305 ( 168) hydrogen bonds : angle 3.97208 ( 498) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 33 time to evaluate : 0.073 Fit side-chains REVERT: R 78 LEU cc_start: 0.6810 (OUTLIER) cc_final: 0.6499 (tp) outliers start: 2 outliers final: 0 residues processed: 34 average time/residue: 0.0708 time to fit residues: 2.8137 Evaluate side-chains 30 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 18 optimal weight: 0.0970 chunk 1 optimal weight: 0.0970 chunk 27 optimal weight: 0.4980 chunk 16 optimal weight: 0.1980 chunk 21 optimal weight: 0.2980 chunk 6 optimal weight: 0.1980 chunk 17 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 11 optimal weight: 0.3980 chunk 5 optimal weight: 0.1980 overall best weight: 0.1576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 HIS R 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.127211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116437 restraints weight = 3220.030| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 1.78 r_work: 0.3468 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2136 Z= 0.136 Angle : 0.668 7.234 2929 Z= 0.329 Chirality : 0.040 0.135 332 Planarity : 0.005 0.048 373 Dihedral : 4.149 21.193 318 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.09 % Allowed : 17.39 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.64 (0.52), residues: 284 helix: 2.21 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -3.10 (0.64), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG R 222 TYR 0.010 0.001 TYR R 76 PHE 0.010 0.001 PHE R 107 TRP 0.005 0.001 TRP R 43 HIS 0.002 0.001 HIS R 159 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 2135) covalent geometry : angle 0.66755 ( 2927) SS BOND : bond 0.00115 ( 1) SS BOND : angle 0.80326 ( 2) hydrogen bonds : bond 0.03315 ( 168) hydrogen bonds : angle 3.96244 ( 498) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 32 time to evaluate : 0.076 Fit side-chains REVERT: R 78 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6643 (tp) outliers start: 2 outliers final: 1 residues processed: 33 average time/residue: 0.0722 time to fit residues: 2.7839 Evaluate side-chains 31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 30 LEU Chi-restraints excluded: chain R residue 78 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 0.0270 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 7 optimal weight: 0.2980 chunk 18 optimal weight: 0.0980 chunk 19 optimal weight: 0.4980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 0.9980 chunk 21 optimal weight: 0.1980 chunk 26 optimal weight: 0.7980 overall best weight: 0.1838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 HIS R 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.126486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.115783 restraints weight = 3248.284| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 1.78 r_work: 0.3456 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2136 Z= 0.142 Angle : 0.697 9.446 2929 Z= 0.340 Chirality : 0.040 0.141 332 Planarity : 0.006 0.052 373 Dihedral : 4.214 21.211 318 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.54 % Allowed : 19.02 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.65 (0.52), residues: 284 helix: 2.21 (0.36), residues: 219 sheet: None (None), residues: 0 loop : -3.09 (0.64), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 222 TYR 0.011 0.001 TYR R 76 PHE 0.010 0.001 PHE R 107 TRP 0.005 0.001 TRP R 43 HIS 0.002 0.001 HIS R 159 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 2135) covalent geometry : angle 0.69660 ( 2927) SS BOND : bond 0.00116 ( 1) SS BOND : angle 0.78017 ( 2) hydrogen bonds : bond 0.03365 ( 168) hydrogen bonds : angle 3.97733 ( 498) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 31 time to evaluate : 0.078 Fit side-chains REVERT: R 78 LEU cc_start: 0.6944 (OUTLIER) cc_final: 0.6673 (tp) REVERT: R 284 LEU cc_start: 0.8095 (tt) cc_final: 0.7761 (tp) outliers start: 1 outliers final: 0 residues processed: 32 average time/residue: 0.0727 time to fit residues: 2.7190 Evaluate side-chains 30 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 3 optimal weight: 0.0870 chunk 12 optimal weight: 0.2980 chunk 4 optimal weight: 0.3980 chunk 6 optimal weight: 0.6980 chunk 5 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 chunk 18 optimal weight: 0.0770 chunk 19 optimal weight: 0.3980 chunk 0 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 0.2316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 HIS R 164 ASN ** R 276 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.125488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115290 restraints weight = 3310.979| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.74 r_work: 0.3444 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3327 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2136 Z= 0.153 Angle : 0.698 8.523 2929 Z= 0.343 Chirality : 0.041 0.154 332 Planarity : 0.005 0.048 373 Dihedral : 4.278 20.864 318 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.72 % Allowed : 16.85 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.59 (0.52), residues: 284 helix: 2.18 (0.35), residues: 219 sheet: None (None), residues: 0 loop : -3.13 (0.66), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 222 TYR 0.011 0.001 TYR R 76 PHE 0.011 0.001 PHE R 107 TRP 0.006 0.001 TRP R 73 HIS 0.002 0.001 HIS R 159 Details of bonding type rmsd covalent geometry : bond 0.00381 ( 2135) covalent geometry : angle 0.69804 ( 2927) SS BOND : bond 0.00070 ( 1) SS BOND : angle 0.75269 ( 2) hydrogen bonds : bond 0.03526 ( 168) hydrogen bonds : angle 4.04070 ( 498) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.044 Fit side-chains REVERT: R 78 LEU cc_start: 0.7087 (OUTLIER) cc_final: 0.6835 (tp) REVERT: R 284 LEU cc_start: 0.8145 (tt) cc_final: 0.7825 (tp) outliers start: 5 outliers final: 0 residues processed: 31 average time/residue: 0.0758 time to fit residues: 2.7331 Evaluate side-chains 29 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 78 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.0980 chunk 23 optimal weight: 0.2980 chunk 11 optimal weight: 0.0060 chunk 1 optimal weight: 0.5980 chunk 13 optimal weight: 0.0870 chunk 0 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 chunk 6 optimal weight: 0.0970 chunk 17 optimal weight: 0.1980 chunk 21 optimal weight: 0.1980 overall best weight: 0.0750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 HIS R 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.129691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.119118 restraints weight = 3259.283| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.79 r_work: 0.3513 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.2880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2136 Z= 0.127 Angle : 0.661 8.470 2929 Z= 0.323 Chirality : 0.039 0.136 332 Planarity : 0.005 0.048 373 Dihedral : 4.113 20.901 318 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.54 % Allowed : 20.65 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.70 (0.52), residues: 284 helix: 2.24 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -3.12 (0.64), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 222 TYR 0.011 0.001 TYR R 76 PHE 0.010 0.001 PHE R 107 TRP 0.005 0.001 TRP R 40 HIS 0.002 0.001 HIS R 159 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2135) covalent geometry : angle 0.66115 ( 2927) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.56655 ( 2) hydrogen bonds : bond 0.02962 ( 168) hydrogen bonds : angle 3.86851 ( 498) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.082 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.0563 time to fit residues: 2.3192 Evaluate side-chains 30 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.0070 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.0980 chunk 12 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 18 optimal weight: 0.4980 chunk 13 optimal weight: 0.0970 chunk 2 optimal weight: 0.6980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.125460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115351 restraints weight = 3310.407| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 1.71 r_work: 0.3445 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2136 Z= 0.163 Angle : 0.737 9.565 2929 Z= 0.363 Chirality : 0.042 0.173 332 Planarity : 0.005 0.047 373 Dihedral : 4.328 21.271 318 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 0.54 % Allowed : 21.20 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.60 (0.51), residues: 284 helix: 2.15 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -3.11 (0.64), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 222 TYR 0.011 0.001 TYR R 76 PHE 0.011 0.001 PHE R 107 TRP 0.005 0.001 TRP R 43 HIS 0.003 0.001 HIS R 242 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 2135) covalent geometry : angle 0.73711 ( 2927) SS BOND : bond 0.00028 ( 1) SS BOND : angle 0.59651 ( 2) hydrogen bonds : bond 0.03618 ( 168) hydrogen bonds : angle 4.04456 ( 498) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 568 Ramachandran restraints generated. 284 Oldfield, 0 Emsley, 284 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.069 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 31 average time/residue: 0.0747 time to fit residues: 2.6863 Evaluate side-chains 31 residues out of total 223 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 141 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 24 optimal weight: 0.1980 chunk 14 optimal weight: 0.7980 chunk 18 optimal weight: 0.0470 chunk 2 optimal weight: 0.6980 chunk 1 optimal weight: 0.5980 chunk 6 optimal weight: 0.0770 chunk 5 optimal weight: 0.0980 chunk 25 optimal weight: 0.0980 chunk 19 optimal weight: 0.6980 overall best weight: 0.1036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 HIS R 164 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.129114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.118326 restraints weight = 3321.228| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.80 r_work: 0.3493 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2136 Z= 0.135 Angle : 0.691 8.136 2929 Z= 0.342 Chirality : 0.040 0.158 332 Planarity : 0.006 0.067 373 Dihedral : 4.190 21.352 318 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 1.63 % Allowed : 21.74 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.76 (0.51), residues: 284 helix: 2.28 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -3.10 (0.64), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG R 222 TYR 0.010 0.001 TYR R 76 PHE 0.010 0.001 PHE R 107 TRP 0.005 0.001 TRP R 43 HIS 0.002 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 2135) covalent geometry : angle 0.69132 ( 2927) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.44845 ( 2) hydrogen bonds : bond 0.03042 ( 168) hydrogen bonds : angle 3.89511 ( 498) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 815.87 seconds wall clock time: 14 minutes 42.66 seconds (882.66 seconds total)