Starting phenix.real_space_refine on Tue Mar 3 13:03:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sb2_24961/03_2026/7sb2_24961.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sb2_24961/03_2026/7sb2_24961.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7sb2_24961/03_2026/7sb2_24961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sb2_24961/03_2026/7sb2_24961.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7sb2_24961/03_2026/7sb2_24961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sb2_24961/03_2026/7sb2_24961.map" } resolution = 3.4 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= 0.004 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 17 5.16 5 C 2956 2.51 5 N 787 2.21 5 O 955 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4715 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2357 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 5, 'TRANS': 293} Chain: "B" Number of atoms: 2358 Number of conformers: 1 Conformer: "" Number of residues, atoms: 299, 2358 Classifications: {'peptide': 299} Link IDs: {'PTRANS': 6, 'TRANS': 292} Time building chain proxies: 1.11, per 1000 atoms: 0.24 Number of scatterers: 4715 At special positions: 0 Unit cell: (69.216, 64.272, 118.656, 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 17 16.00 O 955 8.00 N 787 7.00 C 2956 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: 0.30 Conformation dependent library (CDL) restraints added in 318.8 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1090 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 8 sheets defined 52.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.14 Creating SS restraints... Processing helix chain 'A' and resid 32 through 66 Processing helix chain 'A' and resid 67 through 104 removed outlier: 3.561A pdb=" N PHE A 71 " --> pdb=" O ASN A 67 " (cutoff:3.500A) removed outlier: 5.375A pdb=" N GLU A 73 " --> pdb=" O ASP A 69 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ALA A 74 " --> pdb=" O GLN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 123 Processing helix chain 'A' and resid 130 through 152 Processing helix chain 'A' and resid 159 through 169 Processing helix chain 'A' and resid 183 through 190 Processing helix chain 'A' and resid 193 through 229 Processing helix chain 'B' and resid 33 through 67 Processing helix chain 'B' and resid 67 through 103 removed outlier: 5.493A pdb=" N GLU B 73 " --> pdb=" O ASP B 69 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N ALA B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL B 103 " --> pdb=" O VAL B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 132 through 151 Processing helix chain 'B' and resid 158 through 169 Processing helix chain 'B' and resid 183 through 189 Processing helix chain 'B' and resid 193 through 228 Processing helix chain 'B' and resid 229 through 231 No H-bonds generated for 'chain 'B' and resid 229 through 231' Processing sheet with id=AA1, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 237 Processing sheet with id=AA3, first strand: chain 'A' and resid 267 through 271 Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA5, first strand: chain 'B' and resid 124 through 125 Processing sheet with id=AA6, first strand: chain 'B' and resid 174 through 175 Processing sheet with id=AA7, first strand: chain 'B' and resid 233 through 238 removed outlier: 3.562A pdb=" N GLU B 238 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA B 253 " --> pdb=" O GLU B 238 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 267 through 269 299 hydrogen bonds defined for protein. 870 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: 0.70 Time building geometry restraints manager: 0.39 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: 1598 1.34 - 1.46: 796 1.46 - 1.57: 2358 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 4786 Sorted by residual: bond pdb=" CB VAL B 81 " pdb=" CG1 VAL B 81 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" C LEU B 307 " pdb=" N TYR B 308 " ideal model delta sigma weight residual 1.331 1.314 0.017 1.44e-02 4.82e+03 1.37e+00 bond pdb=" CA LEU B 291 " pdb=" CB LEU B 291 " ideal model delta sigma weight residual 1.526 1.509 0.018 1.53e-02 4.27e+03 1.33e+00 bond pdb=" CG GLU B 47 " pdb=" CD GLU B 47 " ideal model delta sigma weight residual 1.516 1.488 0.028 2.50e-02 1.60e+03 1.27e+00 bond pdb=" N VAL A 174 " pdb=" CA VAL A 174 " ideal model delta sigma weight residual 1.458 1.444 0.014 1.24e-02 6.50e+03 1.22e+00 ... (remaining 4781 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 6121 1.64 - 3.27: 249 3.27 - 4.91: 49 4.91 - 6.55: 6 6.55 - 8.18: 2 Bond angle restraints: 6427 Sorted by residual: angle pdb=" N LYS A 288 " pdb=" CA LYS A 288 " pdb=" C LYS A 288 " ideal model delta sigma weight residual 110.59 106.09 4.50 1.45e+00 4.76e-01 9.63e+00 angle pdb=" N VAL B 268 " pdb=" CA VAL B 268 " pdb=" CB VAL B 268 " ideal model delta sigma weight residual 112.65 109.59 3.06 1.00e+00 1.00e+00 9.34e+00 angle pdb=" N GLU B 47 " pdb=" CA GLU B 47 " pdb=" CB GLU B 47 " ideal model delta sigma weight residual 110.12 114.50 -4.38 1.47e+00 4.63e-01 8.86e+00 angle pdb=" C PHE B 282 " pdb=" N GLN B 283 " pdb=" CA GLN B 283 " ideal model delta sigma weight residual 121.54 127.07 -5.53 1.91e+00 2.74e-01 8.39e+00 angle pdb=" CB MET B 38 " pdb=" CG MET B 38 " pdb=" SD MET B 38 " ideal model delta sigma weight residual 112.70 104.52 8.18 3.00e+00 1.11e-01 7.44e+00 ... (remaining 6422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 2528 16.50 - 33.00: 306 33.00 - 49.49: 51 49.49 - 65.99: 12 65.99 - 82.49: 8 Dihedral angle restraints: 2905 sinusoidal: 1191 harmonic: 1714 Sorted by residual: dihedral pdb=" CA PHE B 282 " pdb=" C PHE B 282 " pdb=" N GLN B 283 " pdb=" CA GLN B 283 " ideal model delta harmonic sigma weight residual 180.00 -152.34 -27.66 0 5.00e+00 4.00e-02 3.06e+01 dihedral pdb=" CA ALA A 279 " pdb=" C ALA A 279 " pdb=" N SER A 280 " pdb=" CA SER A 280 " ideal model delta harmonic sigma weight residual -180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET A 230 " pdb=" C MET A 230 " pdb=" N THR A 231 " pdb=" CA THR A 231 " ideal model delta harmonic sigma weight residual 180.00 161.46 18.54 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 380 0.030 - 0.061: 191 0.061 - 0.091: 76 0.091 - 0.122: 21 0.122 - 0.152: 11 Chirality restraints: 679 Sorted by residual: chirality pdb=" CA ARG B 275 " pdb=" N ARG B 275 " pdb=" C ARG B 275 " pdb=" CB ARG B 275 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CG LEU A 236 " pdb=" CB LEU A 236 " pdb=" CD1 LEU A 236 " pdb=" CD2 LEU A 236 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA VAL B 318 " pdb=" N VAL B 318 " pdb=" C VAL B 318 " pdb=" CB VAL B 318 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.87e-01 ... (remaining 676 not shown) Planarity restraints: 859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR B 244 " 0.007 2.00e-02 2.50e+03 1.46e-02 2.13e+00 pdb=" C TYR B 244 " -0.025 2.00e-02 2.50e+03 pdb=" O TYR B 244 " 0.009 2.00e-02 2.50e+03 pdb=" N TYR B 245 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN A 213 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C GLN A 213 " -0.024 2.00e-02 2.50e+03 pdb=" O GLN A 213 " 0.009 2.00e-02 2.50e+03 pdb=" N GLU A 214 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 72 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.70e+00 pdb=" C ALA A 72 " 0.023 2.00e-02 2.50e+03 pdb=" O ALA A 72 " -0.008 2.00e-02 2.50e+03 pdb=" N GLU A 73 " -0.008 2.00e-02 2.50e+03 ... (remaining 856 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 415 2.72 - 3.27: 5638 3.27 - 3.81: 8488 3.81 - 4.36: 10038 4.36 - 4.90: 16378 Nonbonded interactions: 40957 Sorted by model distance: nonbonded pdb=" OE1 GLU B 212 " pdb=" OH TYR B 216 " model vdw 2.178 3.040 nonbonded pdb=" O GLU B 98 " pdb=" NE2 GLN B 102 " model vdw 2.182 3.120 nonbonded pdb=" O GLU A 248 " pdb=" ND2 ASN B 297 " model vdw 2.185 3.120 nonbonded pdb=" NZ LYS A 154 " pdb=" OD2 ASP A 166 " model vdw 2.193 3.120 nonbonded pdb=" O GLN B 223 " pdb=" OG SER B 226 " model vdw 2.222 3.040 ... (remaining 40952 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 30 through 325) selection = (chain 'B' and resid 30 through 325) } 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: 0.840 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.220 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 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 0.046 4786 Z= 0.327 Angle : 0.787 8.184 6427 Z= 0.436 Chirality : 0.044 0.152 679 Planarity : 0.004 0.030 859 Dihedral : 14.924 82.489 1815 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.42 % Favored : 91.41 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.29 (0.34), residues: 594 helix: 1.69 (0.29), residues: 296 sheet: -0.99 (0.57), residues: 82 loop : -2.68 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG B 275 TYR 0.021 0.002 TYR A 158 PHE 0.019 0.002 PHE B 136 TRP 0.008 0.002 TRP B 184 HIS 0.001 0.001 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00678 ( 4786) covalent geometry : angle 0.78658 ( 6427) hydrogen bonds : bond 0.10516 ( 299) hydrogen bonds : angle 6.17984 ( 870) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 LEU cc_start: 0.8736 (tp) cc_final: 0.8417 (tp) REVERT: B 233 TYR cc_start: 0.7285 (m-80) cc_final: 0.6726 (m-80) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0664 time to fit residues: 4.3795 Evaluate side-chains 43 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 54 optimal weight: 0.0770 chunk 24 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 9.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 141 ASN B 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.057932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.042982 restraints weight = 20034.609| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 4.38 r_work: 0.2789 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4786 Z= 0.138 Angle : 0.656 7.087 6427 Z= 0.341 Chirality : 0.042 0.140 679 Planarity : 0.003 0.036 859 Dihedral : 5.177 28.385 640 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.35), residues: 594 helix: 2.30 (0.29), residues: 300 sheet: -0.98 (0.58), residues: 80 loop : -2.33 (0.38), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 264 TYR 0.012 0.001 TYR B 245 PHE 0.013 0.002 PHE B 136 TRP 0.004 0.001 TRP A 184 HIS 0.002 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4786) covalent geometry : angle 0.65586 ( 6427) hydrogen bonds : bond 0.04408 ( 299) hydrogen bonds : angle 4.99119 ( 870) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.137 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.9162 (m-30) cc_final: 0.8949 (m-30) REVERT: B 282 PHE cc_start: 0.9281 (m-80) cc_final: 0.9061 (m-80) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.0872 time to fit residues: 5.8358 Evaluate side-chains 41 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 GLN ** B 297 ASN ** 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 = 0.3406 r_free = 0.3406 target = 0.058167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.043261 restraints weight = 20207.042| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 4.48 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4786 Z= 0.134 Angle : 0.611 8.200 6427 Z= 0.319 Chirality : 0.041 0.132 679 Planarity : 0.003 0.042 859 Dihedral : 4.875 25.354 640 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.79 % Allowed : 12.48 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.35), residues: 594 helix: 2.50 (0.28), residues: 300 sheet: -1.05 (0.56), residues: 80 loop : -2.21 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 275 TYR 0.014 0.001 TYR B 245 PHE 0.013 0.001 PHE B 136 TRP 0.003 0.001 TRP B 184 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4786) covalent geometry : angle 0.61075 ( 6427) hydrogen bonds : bond 0.04098 ( 299) hydrogen bonds : angle 4.69338 ( 870) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8246 (mpp) cc_final: 0.7871 (mpp) REVERT: A 203 MET cc_start: 0.8442 (OUTLIER) cc_final: 0.7850 (mtp) REVERT: A 207 ASP cc_start: 0.8717 (m-30) cc_final: 0.8480 (m-30) REVERT: B 216 TYR cc_start: 0.9057 (m-10) cc_final: 0.8822 (m-10) REVERT: B 282 PHE cc_start: 0.9186 (m-80) cc_final: 0.8838 (m-80) outliers start: 4 outliers final: 0 residues processed: 52 average time/residue: 0.0666 time to fit residues: 4.6919 Evaluate side-chains 41 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 232 ASN ** B 297 ASN ** 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 = 0.3387 r_free = 0.3387 target = 0.057259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.042685 restraints weight = 20602.708| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 4.49 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 4786 Z= 0.176 Angle : 0.620 8.208 6427 Z= 0.324 Chirality : 0.041 0.199 679 Planarity : 0.004 0.041 859 Dihedral : 4.792 24.789 640 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.19 % Allowed : 14.46 % Favored : 84.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.34), residues: 594 helix: 2.51 (0.28), residues: 300 sheet: -1.06 (0.55), residues: 79 loop : -2.16 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 264 TYR 0.014 0.001 TYR B 245 PHE 0.015 0.001 PHE B 136 TRP 0.006 0.002 TRP A 184 HIS 0.001 0.001 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 4786) covalent geometry : angle 0.61969 ( 6427) hydrogen bonds : bond 0.04148 ( 299) hydrogen bonds : angle 4.76612 ( 870) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 47 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8358 (mpp) cc_final: 0.7856 (mpp) REVERT: A 203 MET cc_start: 0.8367 (OUTLIER) cc_final: 0.7846 (ttp) REVERT: A 207 ASP cc_start: 0.8734 (m-30) cc_final: 0.8478 (m-30) REVERT: B 187 TYR cc_start: 0.8867 (t80) cc_final: 0.8667 (t80) REVERT: B 282 PHE cc_start: 0.9154 (m-80) cc_final: 0.8741 (m-80) outliers start: 6 outliers final: 2 residues processed: 50 average time/residue: 0.0603 time to fit residues: 4.1527 Evaluate side-chains 45 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 203 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 0.5980 chunk 15 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN ** B 297 ASN ** 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 = 0.3406 r_free = 0.3406 target = 0.058158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.043430 restraints weight = 20306.874| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 4.48 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.2467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4786 Z= 0.130 Angle : 0.591 7.971 6427 Z= 0.310 Chirality : 0.040 0.131 679 Planarity : 0.003 0.030 859 Dihedral : 4.647 23.818 640 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 0.99 % Allowed : 17.03 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.35), residues: 594 helix: 2.57 (0.28), residues: 300 sheet: -1.07 (0.56), residues: 79 loop : -2.01 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 264 TYR 0.021 0.001 TYR A 158 PHE 0.013 0.001 PHE B 136 TRP 0.003 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4786) covalent geometry : angle 0.59138 ( 6427) hydrogen bonds : bond 0.03982 ( 299) hydrogen bonds : angle 4.58888 ( 870) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 47 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.7766 (ttp) REVERT: A 207 ASP cc_start: 0.8773 (m-30) cc_final: 0.8373 (m-30) REVERT: A 212 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.7912 (tt0) REVERT: B 282 PHE cc_start: 0.9245 (m-80) cc_final: 0.8795 (m-80) outliers start: 5 outliers final: 3 residues processed: 50 average time/residue: 0.0711 time to fit residues: 4.6506 Evaluate side-chains 47 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 40 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 5.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.057871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.043114 restraints weight = 20539.692| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.58 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4786 Z= 0.158 Angle : 0.604 7.578 6427 Z= 0.315 Chirality : 0.040 0.130 679 Planarity : 0.003 0.028 859 Dihedral : 4.611 23.424 640 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.58 % Allowed : 17.03 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.35), residues: 594 helix: 2.60 (0.28), residues: 300 sheet: -1.12 (0.55), residues: 79 loop : -1.97 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 264 TYR 0.020 0.001 TYR A 158 PHE 0.015 0.001 PHE B 136 TRP 0.006 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 4786) covalent geometry : angle 0.60400 ( 6427) hydrogen bonds : bond 0.04021 ( 299) hydrogen bonds : angle 4.59276 ( 870) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 48 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8315 (OUTLIER) cc_final: 0.7719 (ttp) REVERT: A 207 ASP cc_start: 0.8783 (m-30) cc_final: 0.8395 (m-30) REVERT: A 212 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8028 (tt0) REVERT: B 282 PHE cc_start: 0.9233 (m-80) cc_final: 0.8784 (m-80) outliers start: 8 outliers final: 5 residues processed: 53 average time/residue: 0.0615 time to fit residues: 4.4643 Evaluate side-chains 48 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 212 GLU Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 34 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 27 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.058319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.043576 restraints weight = 20111.490| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.47 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4786 Z= 0.127 Angle : 0.616 7.994 6427 Z= 0.315 Chirality : 0.040 0.132 679 Planarity : 0.003 0.029 859 Dihedral : 4.499 22.408 640 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.58 % Allowed : 17.03 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.35), residues: 594 helix: 2.60 (0.28), residues: 300 sheet: -1.08 (0.55), residues: 79 loop : -1.84 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 264 TYR 0.017 0.001 TYR A 158 PHE 0.013 0.001 PHE B 136 TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4786) covalent geometry : angle 0.61599 ( 6427) hydrogen bonds : bond 0.03950 ( 299) hydrogen bonds : angle 4.51776 ( 870) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.201 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8320 (OUTLIER) cc_final: 0.7816 (ttp) REVERT: A 207 ASP cc_start: 0.8760 (m-30) cc_final: 0.8368 (m-30) REVERT: B 38 MET cc_start: 0.8583 (mmm) cc_final: 0.7978 (mmm) REVERT: B 187 TYR cc_start: 0.8920 (t80) cc_final: 0.8680 (t80) REVERT: B 282 PHE cc_start: 0.9226 (m-80) cc_final: 0.8767 (m-80) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.0611 time to fit residues: 4.0758 Evaluate side-chains 48 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 7 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 20 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.058136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.043457 restraints weight = 20499.048| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 4.50 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4786 Z= 0.133 Angle : 0.636 8.196 6427 Z= 0.327 Chirality : 0.041 0.207 679 Planarity : 0.003 0.029 859 Dihedral : 4.466 21.807 640 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.39 % Allowed : 18.42 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.35), residues: 594 helix: 2.54 (0.28), residues: 300 sheet: -1.09 (0.55), residues: 79 loop : -1.83 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 264 TYR 0.016 0.001 TYR A 158 PHE 0.013 0.001 PHE B 136 TRP 0.005 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4786) covalent geometry : angle 0.63619 ( 6427) hydrogen bonds : bond 0.03976 ( 299) hydrogen bonds : angle 4.55551 ( 870) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8153 (OUTLIER) cc_final: 0.7614 (mtp) REVERT: A 207 ASP cc_start: 0.8765 (m-30) cc_final: 0.8383 (m-30) REVERT: B 38 MET cc_start: 0.8540 (mmm) cc_final: 0.7860 (mmm) REVERT: B 187 TYR cc_start: 0.8909 (t80) cc_final: 0.8663 (t80) REVERT: B 282 PHE cc_start: 0.9214 (m-80) cc_final: 0.8757 (m-80) outliers start: 7 outliers final: 6 residues processed: 47 average time/residue: 0.0635 time to fit residues: 4.1178 Evaluate side-chains 48 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 9.9990 chunk 46 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 56 optimal weight: 9.9990 chunk 36 optimal weight: 0.4980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.058180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.043628 restraints weight = 20235.561| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.45 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4786 Z= 0.130 Angle : 0.635 9.202 6427 Z= 0.326 Chirality : 0.041 0.134 679 Planarity : 0.003 0.029 859 Dihedral : 4.409 21.365 640 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.58 % Allowed : 17.82 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.35), residues: 594 helix: 2.57 (0.28), residues: 300 sheet: -1.08 (0.55), residues: 79 loop : -1.85 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 264 TYR 0.014 0.001 TYR A 158 PHE 0.013 0.001 PHE B 136 TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4786) covalent geometry : angle 0.63463 ( 6427) hydrogen bonds : bond 0.03935 ( 299) hydrogen bonds : angle 4.49921 ( 870) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.126 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7962 (ttm) REVERT: A 207 ASP cc_start: 0.8769 (m-30) cc_final: 0.8356 (m-30) REVERT: B 187 TYR cc_start: 0.8882 (t80) cc_final: 0.8659 (t80) REVERT: B 282 PHE cc_start: 0.9109 (m-80) cc_final: 0.8687 (m-80) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.0797 time to fit residues: 5.2521 Evaluate side-chains 48 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 14 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 3 optimal weight: 0.8980 chunk 47 optimal weight: 0.6980 chunk 8 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 56 optimal weight: 9.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.058225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.043729 restraints weight = 20252.165| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.45 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8602 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4786 Z= 0.134 Angle : 0.666 9.439 6427 Z= 0.339 Chirality : 0.041 0.201 679 Planarity : 0.003 0.029 859 Dihedral : 4.422 20.986 640 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.39 % Allowed : 18.42 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.35), residues: 594 helix: 2.53 (0.28), residues: 303 sheet: -1.05 (0.56), residues: 79 loop : -1.81 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 264 TYR 0.013 0.001 TYR A 158 PHE 0.013 0.001 PHE B 136 TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 4786) covalent geometry : angle 0.66635 ( 6427) hydrogen bonds : bond 0.03931 ( 299) hydrogen bonds : angle 4.49744 ( 870) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 207 ASP cc_start: 0.8758 (m-30) cc_final: 0.8340 (m-30) REVERT: B 187 TYR cc_start: 0.8905 (t80) cc_final: 0.8680 (t80) REVERT: B 216 TYR cc_start: 0.8930 (m-10) cc_final: 0.8692 (m-10) REVERT: B 282 PHE cc_start: 0.9084 (m-80) cc_final: 0.8668 (m-80) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.0671 time to fit residues: 4.1521 Evaluate side-chains 47 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 268 VAL Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 320 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 36 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 32 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 297 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.058439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.044069 restraints weight = 20474.834| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.50 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4786 Z= 0.133 Angle : 0.662 9.976 6427 Z= 0.336 Chirality : 0.041 0.177 679 Planarity : 0.003 0.029 859 Dihedral : 4.400 20.587 640 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.19 % Allowed : 18.42 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.35), residues: 594 helix: 2.51 (0.28), residues: 304 sheet: -1.07 (0.56), residues: 79 loop : -1.78 (0.40), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 264 TYR 0.013 0.001 TYR A 158 PHE 0.013 0.001 PHE B 136 TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 4786) covalent geometry : angle 0.66248 ( 6427) hydrogen bonds : bond 0.03896 ( 299) hydrogen bonds : angle 4.48628 ( 870) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 919.97 seconds wall clock time: 16 minutes 36.23 seconds (996.23 seconds total)