Starting phenix.real_space_refine on Wed Mar 5 14:44:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7e0f_30931/03_2025/7e0f_30931.cif Found real_map, /net/cci-nas-00/data/ceres_data/7e0f_30931/03_2025/7e0f_30931.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7e0f_30931/03_2025/7e0f_30931.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7e0f_30931/03_2025/7e0f_30931.map" model { file = "/net/cci-nas-00/data/ceres_data/7e0f_30931/03_2025/7e0f_30931.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7e0f_30931/03_2025/7e0f_30931.cif" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 3 Type Number sf(0) Gaussians C 1248 2.51 5 N 354 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2022 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 337 Classifications: {'peptide': 49} Link IDs: {'TRANS': 48} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 2.38, per 1000 atoms: 1.18 Number of scatterers: 2022 At special positions: 0 Unit cell: (79.5, 81.62, 34.98, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 420 8.00 N 354 7.00 C 1248 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 275.5 milliseconds 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA3, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.582A pdb=" N VAL A 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL B 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 75 through 77 removed outlier: 6.344A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 93 through 94 Processing sheet with id=AA6, first strand: chain 'D' and resid 54 through 55 Processing sheet with id=AA7, first strand: chain 'D' and resid 61 through 63 Processing sheet with id=AA8, first strand: chain 'D' and resid 69 through 71 removed outlier: 6.613A pdb=" N VAL D 70 " --> pdb=" O VAL E 71 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL E 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'D' and resid 75 through 77 removed outlier: 6.385A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N ALA E 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'D' and resid 93 through 94 16 hydrogen bonds defined for protein. 48 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: 0.43 Time building geometry restraints manager: 0.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.27: 378 1.27 - 1.34: 312 1.34 - 1.41: 60 1.41 - 1.47: 366 1.47 - 1.54: 912 Bond restraints: 2028 Sorted by residual: bond pdb=" C GLN C 79 " pdb=" N LYS C 80 " ideal model delta sigma weight residual 1.332 1.269 0.064 1.40e-02 5.10e+03 2.06e+01 bond pdb=" C GLN F 79 " pdb=" N LYS F 80 " ideal model delta sigma weight residual 1.332 1.269 0.063 1.40e-02 5.10e+03 2.04e+01 bond pdb=" C GLN D 79 " pdb=" N LYS D 80 " ideal model delta sigma weight residual 1.332 1.269 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" C GLN B 79 " pdb=" N LYS B 80 " ideal model delta sigma weight residual 1.332 1.270 0.063 1.40e-02 5.10e+03 2.02e+01 bond pdb=" C GLN A 79 " pdb=" N LYS A 80 " ideal model delta sigma weight residual 1.332 1.270 0.063 1.40e-02 5.10e+03 2.00e+01 ... (remaining 2023 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.14: 2321 1.14 - 2.28: 337 2.28 - 3.43: 42 3.43 - 4.57: 42 4.57 - 5.71: 6 Bond angle restraints: 2748 Sorted by residual: angle pdb=" C GLY D 93 " pdb=" N PHE D 94 " pdb=" CA PHE D 94 " ideal model delta sigma weight residual 121.58 115.87 5.71 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY B 93 " pdb=" N PHE B 94 " pdb=" CA PHE B 94 " ideal model delta sigma weight residual 121.58 115.87 5.71 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY F 93 " pdb=" N PHE F 94 " pdb=" CA PHE F 94 " ideal model delta sigma weight residual 121.58 115.88 5.70 1.62e+00 3.81e-01 1.24e+01 angle pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta sigma weight residual 121.58 115.89 5.69 1.62e+00 3.81e-01 1.23e+01 angle pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta sigma weight residual 121.58 115.89 5.69 1.62e+00 3.81e-01 1.23e+01 ... (remaining 2743 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 1086 17.15 - 34.29: 84 34.29 - 51.43: 12 51.43 - 68.58: 0 68.58 - 85.72: 12 Dihedral angle restraints: 1194 sinusoidal: 390 harmonic: 804 Sorted by residual: dihedral pdb=" CA GLY A 93 " pdb=" C GLY A 93 " pdb=" N PHE A 94 " pdb=" CA PHE A 94 " ideal model delta harmonic sigma weight residual -180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLY B 93 " pdb=" C GLY B 93 " pdb=" N PHE B 94 " pdb=" CA PHE B 94 " ideal model delta harmonic sigma weight residual 180.00 -153.61 -26.39 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA GLY E 93 " pdb=" C GLY E 93 " pdb=" N PHE E 94 " pdb=" CA PHE E 94 " ideal model delta harmonic sigma weight residual -180.00 -153.64 -26.36 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 1191 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 161 0.043 - 0.085: 128 0.085 - 0.127: 54 0.127 - 0.169: 17 0.169 - 0.211: 6 Chirality restraints: 366 Sorted by residual: chirality pdb=" CB VAL A 95 " pdb=" CA VAL A 95 " pdb=" CG1 VAL A 95 " pdb=" CG2 VAL A 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CB VAL B 95 " pdb=" CA VAL B 95 " pdb=" CG1 VAL B 95 " pdb=" CG2 VAL B 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB VAL E 95 " pdb=" CA VAL E 95 " pdb=" CG1 VAL E 95 " pdb=" CG2 VAL E 95 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.20 2.00e-01 2.50e+01 1.05e+00 ... (remaining 363 not shown) Planarity restraints: 348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 90 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.16e+00 pdb=" C ALA A 90 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA A 90 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA A 91 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 90 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ALA D 90 " 0.025 2.00e-02 2.50e+03 pdb=" O ALA D 90 " -0.010 2.00e-02 2.50e+03 pdb=" N ALA D 91 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 90 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" C ALA C 90 " -0.025 2.00e-02 2.50e+03 pdb=" O ALA C 90 " 0.010 2.00e-02 2.50e+03 pdb=" N ALA C 91 " 0.009 2.00e-02 2.50e+03 ... (remaining 345 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 770 2.85 - 3.36: 1787 3.36 - 3.88: 2984 3.88 - 4.39: 3268 4.39 - 4.90: 6828 Nonbonded interactions: 15637 Sorted by model distance: nonbonded pdb=" OG1 THR D 54 " pdb=" OG1 THR D 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR E 54 " pdb=" OG1 THR E 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR F 54 " pdb=" OG1 THR F 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR B 54 " pdb=" OG1 THR B 64 " model vdw 2.341 3.040 nonbonded pdb=" OG1 THR A 54 " pdb=" OG1 THR A 64 " model vdw 2.341 3.040 ... (remaining 15632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'F' } 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: 0.010 Normalize map: mean=0, sd=1: 1.680 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.330 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 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 : 0.016 0.086 2028 Z= 1.067 Angle : 0.986 5.709 2748 Z= 0.581 Chirality : 0.069 0.211 366 Planarity : 0.003 0.015 348 Dihedral : 15.885 85.718 678 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.40), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.31), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 50 PHE 0.024 0.007 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.193 Fit side-chains REVERT: B 62 GLN cc_start: 0.8853 (pt0) cc_final: 0.8407 (pt0) REVERT: C 62 GLN cc_start: 0.8813 (pt0) cc_final: 0.8532 (pt0) REVERT: C 83 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7340 (pm20) REVERT: E 60 LYS cc_start: 0.7688 (ttmt) cc_final: 0.7419 (mtpt) REVERT: E 62 GLN cc_start: 0.9017 (pt0) cc_final: 0.8721 (pt0) REVERT: F 61 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8047 (mt-10) REVERT: F 62 GLN cc_start: 0.8878 (pt0) cc_final: 0.8589 (pt0) REVERT: F 83 GLU cc_start: 0.8210 (mm-30) cc_final: 0.7547 (pm20) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1768 time to fit residues: 8.2285 Evaluate side-chains 22 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.205890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.149284 restraints weight = 1975.749| |-----------------------------------------------------------------------------| r_work (start): 0.4266 rms_B_bonded: 3.04 r_work: 0.4139 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2028 Z= 0.187 Angle : 0.592 4.708 2748 Z= 0.331 Chirality : 0.051 0.126 366 Planarity : 0.002 0.009 348 Dihedral : 5.405 24.767 288 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 4.90 % Allowed : 15.69 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.48 (0.44), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS C 50 PHE 0.015 0.004 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.191 Fit side-chains REVERT: B 62 GLN cc_start: 0.8620 (pt0) cc_final: 0.8391 (pt0) REVERT: C 61 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8027 (mt-10) REVERT: C 83 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7303 (pm20) REVERT: F 61 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7987 (mt-10) REVERT: F 83 GLU cc_start: 0.8395 (mm-30) cc_final: 0.7459 (pm20) outliers start: 10 outliers final: 7 residues processed: 49 average time/residue: 0.1046 time to fit residues: 6.2299 Evaluate side-chains 36 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 10 optimal weight: 0.9990 chunk 3 optimal weight: 0.0050 chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN C 62 GLN ** E 62 GLN ** 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 = 0.4799 r_free = 0.4799 target = 0.209463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.151699 restraints weight = 1967.140| |-----------------------------------------------------------------------------| r_work (start): 0.4290 rms_B_bonded: 3.10 r_work: 0.4167 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2028 Z= 0.174 Angle : 0.540 4.150 2748 Z= 0.305 Chirality : 0.049 0.121 366 Planarity : 0.002 0.012 348 Dihedral : 4.873 22.463 288 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.87 % Favored : 91.13 % Rotamer: Outliers : 4.90 % Allowed : 19.61 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.46), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS D 50 PHE 0.012 0.003 PHE B 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 34 time to evaluate : 0.216 Fit side-chains REVERT: B 62 GLN cc_start: 0.8647 (pt0) cc_final: 0.8392 (pt0) REVERT: C 61 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8071 (mt-10) REVERT: C 79 GLN cc_start: 0.9109 (mm-40) cc_final: 0.8837 (mp10) REVERT: C 83 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7255 (pm20) REVERT: D 62 GLN cc_start: 0.8720 (pt0) cc_final: 0.8237 (mt0) REVERT: F 61 GLU cc_start: 0.8288 (mt-10) cc_final: 0.8061 (mt-10) outliers start: 10 outliers final: 9 residues processed: 44 average time/residue: 0.1215 time to fit residues: 6.5047 Evaluate side-chains 41 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 32 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 13 optimal weight: 5.9990 chunk 1 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.1980 chunk 20 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.195308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.135353 restraints weight = 2040.157| |-----------------------------------------------------------------------------| r_work (start): 0.4208 rms_B_bonded: 3.42 r_work: 0.4066 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.4066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2028 Z= 0.204 Angle : 0.514 4.095 2748 Z= 0.291 Chirality : 0.048 0.123 366 Planarity : 0.002 0.018 348 Dihedral : 4.864 22.004 288 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer: Outliers : 6.37 % Allowed : 18.63 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.90 (0.48), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.013 0.003 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.217 Fit side-chains REVERT: B 62 GLN cc_start: 0.8692 (pt0) cc_final: 0.8482 (pt0) REVERT: C 61 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8106 (mt-10) REVERT: C 83 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7168 (pm20) REVERT: F 61 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8052 (mt-10) outliers start: 13 outliers final: 10 residues processed: 42 average time/residue: 0.1033 time to fit residues: 5.3545 Evaluate side-chains 38 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 28 time to evaluate : 0.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 23 optimal weight: 0.0030 chunk 6 optimal weight: 3.9990 chunk 15 optimal weight: 0.0870 chunk 10 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 9.9990 chunk 5 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 overall best weight: 0.5970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 65 ASN F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4755 r_free = 0.4755 target = 0.200711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.138281 restraints weight = 1994.214| |-----------------------------------------------------------------------------| r_work (start): 0.4254 rms_B_bonded: 3.42 r_work: 0.4102 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.4102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2028 Z= 0.141 Angle : 0.476 3.820 2748 Z= 0.270 Chirality : 0.048 0.120 366 Planarity : 0.002 0.018 348 Dihedral : 4.592 20.388 288 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.43 % Allowed : 21.08 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.50), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.77 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.012 0.003 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 30 time to evaluate : 0.208 Fit side-chains REVERT: A 62 GLN cc_start: 0.8578 (pt0) cc_final: 0.8098 (mt0) REVERT: B 62 GLN cc_start: 0.8640 (pt0) cc_final: 0.8336 (mt0) REVERT: C 61 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8097 (mt-10) REVERT: D 62 GLN cc_start: 0.8894 (pt0) cc_final: 0.8675 (mt0) REVERT: D 83 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7805 (mm-30) REVERT: F 61 GLU cc_start: 0.8293 (mt-10) cc_final: 0.8073 (mt-10) outliers start: 7 outliers final: 5 residues processed: 37 average time/residue: 0.1094 time to fit residues: 4.9874 Evaluate side-chains 32 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 27 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN F 62 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4687 r_free = 0.4687 target = 0.193282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.130707 restraints weight = 1978.879| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 3.40 r_work: 0.4005 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 2028 Z= 0.343 Angle : 0.543 4.775 2748 Z= 0.311 Chirality : 0.049 0.126 366 Planarity : 0.002 0.014 348 Dihedral : 5.195 24.189 288 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.57 % Favored : 90.43 % Rotamer: Outliers : 6.37 % Allowed : 18.63 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.65 (0.49), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.78 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.018 0.004 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 29 time to evaluate : 0.196 Fit side-chains REVERT: A 79 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8369 (mt0) REVERT: B 62 GLN cc_start: 0.8774 (pt0) cc_final: 0.8560 (pt0) REVERT: C 61 GLU cc_start: 0.8461 (mt-10) cc_final: 0.8137 (mt-10) REVERT: C 83 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7221 (pm20) REVERT: D 62 GLN cc_start: 0.8929 (pt0) cc_final: 0.8621 (mt0) REVERT: D 83 GLU cc_start: 0.8316 (mm-30) cc_final: 0.7925 (mm-30) outliers start: 13 outliers final: 11 residues processed: 40 average time/residue: 0.1062 time to fit residues: 5.2716 Evaluate side-chains 39 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 27 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 0.0060 chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 15 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN E 79 GLN F 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.202420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.140278 restraints weight = 1952.791| |-----------------------------------------------------------------------------| r_work (start): 0.4281 rms_B_bonded: 3.38 r_work: 0.4135 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2028 Z= 0.125 Angle : 0.465 4.459 2748 Z= 0.264 Chirality : 0.048 0.121 366 Planarity : 0.002 0.013 348 Dihedral : 4.457 19.935 288 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.92 % Allowed : 21.08 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.52 (0.50), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.38), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.012 0.003 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 31 time to evaluate : 0.219 Fit side-chains REVERT: A 62 GLN cc_start: 0.8800 (pt0) cc_final: 0.8265 (mt0) REVERT: B 62 GLN cc_start: 0.8675 (pt0) cc_final: 0.8361 (mt0) REVERT: B 79 GLN cc_start: 0.8945 (OUTLIER) cc_final: 0.8544 (mt0) REVERT: C 61 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8124 (mt-10) REVERT: D 62 GLN cc_start: 0.8850 (pt0) cc_final: 0.8529 (mt0) REVERT: D 83 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7885 (mm-30) REVERT: E 79 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.8133 (mt0) outliers start: 8 outliers final: 5 residues processed: 36 average time/residue: 0.1122 time to fit residues: 4.9797 Evaluate side-chains 34 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 16 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 0 optimal weight: 0.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 79 GLN E 62 GLN F 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.202673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.140946 restraints weight = 1986.719| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 3.26 r_work: 0.4023 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 2028 Z= 0.488 Angle : 0.637 4.889 2748 Z= 0.368 Chirality : 0.052 0.125 366 Planarity : 0.003 0.013 348 Dihedral : 5.503 25.627 288 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.99 % Favored : 89.01 % Rotamer: Outliers : 7.35 % Allowed : 17.16 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.47), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 50 PHE 0.021 0.005 PHE C 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 28 time to evaluate : 0.217 Fit side-chains REVERT: A 79 GLN cc_start: 0.9143 (OUTLIER) cc_final: 0.8381 (mt0) REVERT: C 61 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8109 (mt-10) REVERT: C 79 GLN cc_start: 0.9196 (OUTLIER) cc_final: 0.8317 (mt0) REVERT: C 83 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7294 (pm20) REVERT: D 83 GLU cc_start: 0.8374 (mm-30) cc_final: 0.8126 (mm-30) REVERT: E 79 GLN cc_start: 0.9034 (OUTLIER) cc_final: 0.8110 (mt0) outliers start: 15 outliers final: 11 residues processed: 40 average time/residue: 0.1062 time to fit residues: 5.2373 Evaluate side-chains 40 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 26 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 79 GLN Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 20 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 10.0000 chunk 6 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN E 62 GLN ** F 62 GLN ** 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 = 0.4819 r_free = 0.4819 target = 0.211180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.150579 restraints weight = 1976.098| |-----------------------------------------------------------------------------| r_work (start): 0.4245 rms_B_bonded: 3.16 r_work: 0.4106 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2028 Z= 0.195 Angle : 0.506 4.682 2748 Z= 0.286 Chirality : 0.048 0.123 366 Planarity : 0.002 0.017 348 Dihedral : 4.810 22.210 288 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 4.41 % Allowed : 22.06 % Favored : 73.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.58 (0.49), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.72 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.014 0.004 PHE E 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 27 time to evaluate : 0.229 Fit side-chains REVERT: A 83 GLU cc_start: 0.8046 (mp0) cc_final: 0.7732 (mm-30) REVERT: B 62 GLN cc_start: 0.8603 (pt0) cc_final: 0.8342 (mt0) REVERT: B 79 GLN cc_start: 0.9138 (mm-40) cc_final: 0.8612 (mt0) REVERT: C 61 GLU cc_start: 0.8487 (mt-10) cc_final: 0.8150 (mt-10) REVERT: D 62 GLN cc_start: 0.8764 (OUTLIER) cc_final: 0.8551 (mt0) REVERT: D 83 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7873 (mm-30) outliers start: 9 outliers final: 7 residues processed: 34 average time/residue: 0.1080 time to fit residues: 4.5349 Evaluate side-chains 33 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 21 optimal weight: 0.0370 chunk 16 optimal weight: 9.9990 chunk 3 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 overall best weight: 1.3062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN E 62 GLN ** F 62 GLN ** 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 = 0.4807 r_free = 0.4807 target = 0.209474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.148098 restraints weight = 1944.924| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 3.18 r_work: 0.4116 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2028 Z= 0.263 Angle : 0.518 4.663 2748 Z= 0.295 Chirality : 0.049 0.124 366 Planarity : 0.002 0.016 348 Dihedral : 4.936 22.694 288 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 5.39 % Allowed : 21.57 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.56 (0.49), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.71 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.016 0.004 PHE E 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 564 Ramachandran restraints generated. 282 Oldfield, 0 Emsley, 282 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 24 time to evaluate : 0.239 Fit side-chains REVERT: A 83 GLU cc_start: 0.8137 (mp0) cc_final: 0.7719 (mm-30) REVERT: B 62 GLN cc_start: 0.8634 (pt0) cc_final: 0.8386 (mt0) REVERT: C 61 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8141 (mt-10) REVERT: D 83 GLU cc_start: 0.8339 (mm-30) cc_final: 0.7886 (mm-30) REVERT: E 79 GLN cc_start: 0.8928 (OUTLIER) cc_final: 0.8134 (mt0) outliers start: 11 outliers final: 9 residues processed: 32 average time/residue: 0.0975 time to fit residues: 4.0021 Evaluate side-chains 34 residues out of total 204 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 24 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 62 GLN Chi-restraints excluded: chain E residue 79 GLN Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 24 random chunks: chunk 2 optimal weight: 0.0980 chunk 16 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 4 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 GLN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.205763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.144738 restraints weight = 1954.199| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 3.10 r_work: 0.4082 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.4082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 2028 Z= 0.346 Angle : 0.550 4.629 2748 Z= 0.315 Chirality : 0.050 0.126 366 Planarity : 0.002 0.014 348 Dihedral : 5.157 24.403 288 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.93 % Favored : 90.07 % Rotamer: Outliers : 6.86 % Allowed : 20.10 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.61 (0.48), residues: 282 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.75 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 50 PHE 0.018 0.005 PHE E 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1591.26 seconds wall clock time: 28 minutes 9.15 seconds (1689.15 seconds total)