Starting phenix.real_space_refine on Tue Feb 11 07:59:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sb2_24961/02_2025/7sb2_24961.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sb2_24961/02_2025/7sb2_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7sb2_24961/02_2025/7sb2_24961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sb2_24961/02_2025/7sb2_24961.map" model { file = "/net/cci-nas-00/data/ceres_data/7sb2_24961/02_2025/7sb2_24961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sb2_24961/02_2025/7sb2_24961.cif" } resolution = 3.4 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= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 3.37, per 1000 atoms: 0.71 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: 1.25 Conformation dependent library (CDL) restraints added in 493.9 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: 0.46 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: 1.33 Time building geometry restraints manager: 1.44 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: 0.530 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: 0.020 Extract box with map and model: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.190 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.020 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.090 ------------------------------------------------------------------------------- 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= 0.434 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 : 23.65 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 (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: -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 TRP 0.008 0.002 TRP B 184 HIS 0.001 0.001 HIS B 301 PHE 0.019 0.002 PHE B 136 TYR 0.021 0.002 TYR A 158 ARG 0.019 0.002 ARG B 275 *********************** 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 : 0.590 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: 0.1878 time to fit residues: 12.3415 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 : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 15 optimal weight: 0.0670 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 0.0770 chunk 45 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 3.9990 overall best weight: 0.5476 ------------------------------------------------------------------------------- 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 = 0.3412 r_free = 0.3412 target = 0.057895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042985 restraints weight = 19863.926| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.36 r_work: 0.2785 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4786 Z= 0.179 Angle : 0.658 6.843 6427 Z= 0.342 Chirality : 0.042 0.141 679 Planarity : 0.003 0.035 859 Dihedral : 5.186 28.587 640 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % 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: 0.38 (0.35), residues: 594 helix: 2.27 (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 TRP 0.005 0.001 TRP A 184 HIS 0.002 0.001 HIS A 301 PHE 0.012 0.002 PHE B 136 TYR 0.012 0.001 TYR B 245 ARG 0.005 0.001 ARG B 264 *********************** 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 52 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.550 Fit side-chains revert: symmetry clash REVERT: A 207 ASP cc_start: 0.9145 (m-30) cc_final: 0.8923 (m-30) REVERT: B 187 TYR cc_start: 0.8945 (t80) cc_final: 0.8730 (t80) REVERT: B 282 PHE cc_start: 0.9305 (m-80) cc_final: 0.9101 (m-80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1880 time to fit residues: 12.7828 Evaluate side-chains 42 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 42 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 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 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 = 0.3379 r_free = 0.3379 target = 0.057138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.042260 restraints weight = 20302.573| |-----------------------------------------------------------------------------| r_work (start): 0.2927 rms_B_bonded: 4.43 r_work: 0.2756 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4786 Z= 0.235 Angle : 0.625 8.113 6427 Z= 0.331 Chirality : 0.041 0.130 679 Planarity : 0.004 0.051 859 Dihedral : 5.010 26.288 640 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.79 % Allowed : 12.87 % Favored : 86.34 % 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: 0.54 (0.35), residues: 594 helix: 2.45 (0.28), residues: 300 sheet: -1.09 (0.56), residues: 80 loop : -2.26 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP B 184 HIS 0.001 0.001 HIS A 301 PHE 0.015 0.001 PHE B 136 TYR 0.014 0.001 TYR B 245 ARG 0.006 0.001 ARG B 275 *********************** 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 49 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8523 (mpp) cc_final: 0.8115 (mpp) REVERT: A 203 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8352 (mtp) REVERT: A 207 ASP cc_start: 0.9220 (m-30) cc_final: 0.8995 (m-30) REVERT: B 187 TYR cc_start: 0.8937 (t80) cc_final: 0.8726 (t80) REVERT: B 282 PHE cc_start: 0.9327 (m-80) cc_final: 0.9056 (m-80) outliers start: 4 outliers final: 2 residues processed: 46 average time/residue: 0.1792 time to fit residues: 10.7406 Evaluate side-chains 41 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain B residue 203 MET Chi-restraints excluded: chain B residue 272 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 19 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.058052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.043146 restraints weight = 20300.991| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 4.50 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.2163 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= 0.183 Angle : 0.592 8.130 6427 Z= 0.311 Chirality : 0.040 0.130 679 Planarity : 0.003 0.031 859 Dihedral : 4.765 24.951 640 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.58 % Allowed : 14.46 % Favored : 83.96 % 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: 0.68 (0.35), residues: 594 helix: 2.56 (0.28), residues: 300 sheet: -1.10 (0.55), residues: 79 loop : -2.14 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 PHE 0.013 0.001 PHE B 136 TYR 0.013 0.001 TYR B 245 ARG 0.004 0.001 ARG B 182 *********************** 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 59 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 51 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8364 (mpp) cc_final: 0.7875 (mpp) REVERT: A 203 MET cc_start: 0.8448 (OUTLIER) cc_final: 0.7912 (ttp) REVERT: A 207 ASP cc_start: 0.8712 (m-30) cc_final: 0.8345 (m-30) REVERT: B 282 PHE cc_start: 0.9177 (m-80) cc_final: 0.8766 (m-80) outliers start: 8 outliers final: 1 residues processed: 56 average time/residue: 0.1667 time to fit residues: 12.4908 Evaluate side-chains 44 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 42 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 203 MET Chi-restraints excluded: chain A residue 270 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 39 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 0.4980 chunk 11 optimal weight: 0.0670 chunk 10 optimal weight: 10.0000 chunk 17 optimal weight: 0.6980 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 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 = 0.3422 r_free = 0.3422 target = 0.058805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.043755 restraints weight = 20457.825| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 4.56 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4786 Z= 0.153 Angle : 0.595 7.642 6427 Z= 0.313 Chirality : 0.040 0.132 679 Planarity : 0.003 0.032 859 Dihedral : 4.603 23.263 640 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.39 % Allowed : 16.04 % Favored : 82.57 % 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: 0.80 (0.35), residues: 594 helix: 2.61 (0.28), residues: 300 sheet: -1.10 (0.56), residues: 79 loop : -1.99 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 PHE 0.012 0.001 PHE B 136 TYR 0.021 0.001 TYR A 158 ARG 0.006 0.001 ARG B 264 *********************** 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 59 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8334 (OUTLIER) cc_final: 0.7939 (ttp) REVERT: A 207 ASP cc_start: 0.8750 (m-30) cc_final: 0.8358 (m-30) REVERT: A 212 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.7914 (tt0) REVERT: B 204 MET cc_start: 0.8883 (mtp) cc_final: 0.8585 (mtm) REVERT: B 282 PHE cc_start: 0.9284 (m-80) cc_final: 0.8860 (m-80) outliers start: 7 outliers final: 4 residues processed: 56 average time/residue: 0.1902 time to fit residues: 13.7913 Evaluate side-chains 48 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.587 ------------------------------------------------------------------------------- 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 203 MET 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 57 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 53 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.058195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.043442 restraints weight = 20414.299| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.49 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4786 Z= 0.189 Angle : 0.612 7.451 6427 Z= 0.319 Chirality : 0.041 0.211 679 Planarity : 0.003 0.031 859 Dihedral : 4.566 23.217 640 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.19 % Allowed : 17.43 % 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 (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: 0.82 (0.35), residues: 594 helix: 2.61 (0.28), residues: 300 sheet: -1.12 (0.55), residues: 79 loop : -1.92 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 PHE 0.014 0.001 PHE B 136 TYR 0.019 0.001 TYR A 158 ARG 0.008 0.001 ARG B 264 *********************** 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 51 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8351 (OUTLIER) cc_final: 0.7773 (ttp) REVERT: A 207 ASP cc_start: 0.8769 (m-30) cc_final: 0.8378 (m-30) REVERT: A 212 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.8001 (tt0) REVERT: B 187 TYR cc_start: 0.8889 (t80) cc_final: 0.8640 (t80) REVERT: B 282 PHE cc_start: 0.9252 (m-80) cc_final: 0.8810 (m-80) outliers start: 6 outliers final: 4 residues processed: 48 average time/residue: 0.1598 time to fit residues: 10.4522 Evaluate side-chains 46 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 21 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 = 0.3396 r_free = 0.3396 target = 0.057583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.042957 restraints weight = 20197.053| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 4.48 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2590 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= 0.230 Angle : 0.630 7.747 6427 Z= 0.324 Chirality : 0.042 0.212 679 Planarity : 0.003 0.028 859 Dihedral : 4.607 23.395 640 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.98 % Allowed : 17.23 % Favored : 80.79 % 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: 0.79 (0.35), residues: 594 helix: 2.55 (0.28), residues: 300 sheet: -1.15 (0.55), residues: 79 loop : -1.87 (0.40), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 184 HIS 0.001 0.001 HIS A 301 PHE 0.015 0.001 PHE B 136 TYR 0.017 0.001 TYR A 158 ARG 0.009 0.001 ARG B 264 *********************** 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 54 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.7719 (ttp) REVERT: A 207 ASP cc_start: 0.8759 (m-30) cc_final: 0.8371 (m-30) REVERT: A 212 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7812 (tt0) REVERT: B 38 MET cc_start: 0.8639 (mmm) cc_final: 0.8030 (mmm) REVERT: B 233 TYR cc_start: 0.7993 (m-80) cc_final: 0.7652 (m-80) REVERT: B 282 PHE cc_start: 0.9228 (m-80) cc_final: 0.8774 (m-80) outliers start: 10 outliers final: 6 residues processed: 51 average time/residue: 0.1408 time to fit residues: 10.0191 Evaluate side-chains 49 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.580 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 0 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3406 r_free = 0.3406 target = 0.057953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.043212 restraints weight = 20339.895| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 4.45 r_work: 0.2798 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2758 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= 0.188 Angle : 0.646 8.603 6427 Z= 0.327 Chirality : 0.043 0.260 679 Planarity : 0.003 0.029 859 Dihedral : 4.535 22.792 640 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.98 % Allowed : 17.43 % 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 (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: 0.77 (0.35), residues: 594 helix: 2.50 (0.28), residues: 300 sheet: -1.17 (0.55), residues: 79 loop : -1.81 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 PHE 0.013 0.001 PHE B 136 TYR 0.017 0.001 TYR A 158 ARG 0.008 0.001 ARG B 264 *********************** 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 54 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8827 (OUTLIER) cc_final: 0.8145 (mtp) REVERT: A 207 ASP cc_start: 0.9323 (m-30) cc_final: 0.8987 (m-30) REVERT: A 212 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8025 (tt0) REVERT: B 38 MET cc_start: 0.8828 (mmm) cc_final: 0.8241 (mmm) REVERT: B 187 TYR cc_start: 0.8997 (t80) cc_final: 0.8774 (t80) REVERT: B 233 TYR cc_start: 0.8185 (m-80) cc_final: 0.7851 (m-80) REVERT: B 282 PHE cc_start: 0.9394 (m-80) cc_final: 0.9023 (m-80) outliers start: 10 outliers final: 7 residues processed: 51 average time/residue: 0.1635 time to fit residues: 11.2470 Evaluate side-chains 51 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 201 LEU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 37 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 36 optimal weight: 0.9980 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 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 = 0.3413 r_free = 0.3413 target = 0.058242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.043516 restraints weight = 20331.628| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 4.49 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4786 Z= 0.176 Angle : 0.653 9.183 6427 Z= 0.328 Chirality : 0.043 0.262 679 Planarity : 0.003 0.029 859 Dihedral : 4.455 21.907 640 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.78 % Allowed : 17.82 % 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 (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: 0.79 (0.35), residues: 594 helix: 2.49 (0.28), residues: 300 sheet: -1.14 (0.56), residues: 79 loop : -1.77 (0.41), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS A 301 PHE 0.013 0.001 PHE B 136 TYR 0.015 0.001 TYR A 158 ARG 0.009 0.001 ARG B 264 *********************** 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 53 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8061 (mpp) cc_final: 0.7438 (pmm) REVERT: A 203 MET cc_start: 0.8252 (OUTLIER) cc_final: 0.7936 (ttm) REVERT: A 207 ASP cc_start: 0.8752 (m-30) cc_final: 0.8351 (m-30) REVERT: A 212 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: B 233 TYR cc_start: 0.7813 (m-80) cc_final: 0.7531 (m-80) REVERT: B 282 PHE cc_start: 0.9112 (m-80) cc_final: 0.8691 (m-80) outliers start: 9 outliers final: 7 residues processed: 50 average time/residue: 0.1750 time to fit residues: 11.5670 Evaluate side-chains 50 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 201 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 51 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 57 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 53 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 47 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 56 optimal weight: 0.9990 chunk 14 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 188 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 = 0.3421 r_free = 0.3421 target = 0.058488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.043875 restraints weight = 20011.396| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.45 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4786 Z= 0.169 Angle : 0.683 14.330 6427 Z= 0.337 Chirality : 0.042 0.254 679 Planarity : 0.003 0.031 859 Dihedral : 4.387 21.111 640 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 1.78 % Allowed : 18.02 % 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 (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: 0.80 (0.35), residues: 594 helix: 2.46 (0.28), residues: 303 sheet: -1.04 (0.57), residues: 79 loop : -1.80 (0.41), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 184 HIS 0.000 0.000 HIS A 301 PHE 0.013 0.001 PHE B 136 TYR 0.018 0.001 TYR B 216 ARG 0.009 0.001 ARG B 264 ********************** 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 54 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8060 (mpp) cc_final: 0.7435 (pmm) REVERT: A 203 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7955 (ttm) REVERT: A 207 ASP cc_start: 0.8727 (m-30) cc_final: 0.8332 (m-30) REVERT: A 212 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.7796 (tt0) REVERT: B 233 TYR cc_start: 0.7802 (m-80) cc_final: 0.7445 (m-80) REVERT: B 282 PHE cc_start: 0.9095 (m-80) cc_final: 0.8684 (m-80) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.1513 time to fit residues: 10.5745 Evaluate side-chains 49 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 201 LEU 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 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 38 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 51 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3380 r_free = 0.3380 target = 0.056968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.042333 restraints weight = 20379.561| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 4.40 r_work: 0.2762 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4786 Z= 0.290 Angle : 0.732 12.472 6427 Z= 0.370 Chirality : 0.044 0.282 679 Planarity : 0.004 0.036 859 Dihedral : 4.607 22.837 640 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 15.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 1.98 % Allowed : 18.22 % Favored : 79.80 % 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: 0.63 (0.35), residues: 594 helix: 2.31 (0.28), residues: 303 sheet: -1.12 (0.56), residues: 79 loop : -1.87 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 184 HIS 0.002 0.001 HIS A 301 PHE 0.016 0.002 PHE B 136 TYR 0.014 0.002 TYR A 158 ARG 0.010 0.001 ARG B 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1978.33 seconds wall clock time: 36 minutes 23.87 seconds (2183.87 seconds total)