Starting phenix.real_space_refine on Thu Mar 6 03:55:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7sb2_24961/03_2025/7sb2_24961.cif Found real_map, /net/cci-nas-00/data/ceres_data/7sb2_24961/03_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_24961/03_2025/7sb2_24961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7sb2_24961/03_2025/7sb2_24961.map" model { file = "/net/cci-nas-00/data/ceres_data/7sb2_24961/03_2025/7sb2_24961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7sb2_24961/03_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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.28, per 1000 atoms: 0.70 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: 1.24 Conformation dependent library (CDL) restraints added in 528.4 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: 0.49 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: 1.52 Time building geometry restraints manager: 1.41 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: 0.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 15.800 Find NCS groups from input model: 0.210 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.070 ------------------------------------------------------------------------------- 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 : 0.668 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: 0.1894 time to fit residues: 12.3815 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 : 0.560 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.042981 restraints weight = 19863.920| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 4.37 r_work: 0.2786 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 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 : 0.519 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: 0.9303 (m-80) cc_final: 0.9100 (m-80) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1714 time to fit residues: 11.6972 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 : 0.585 ------------------------------------------------------------------------------- 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: 0.8980 chunk 49 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 22 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3383 r_free = 0.3383 target = 0.057288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.042410 restraints weight = 20239.901| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 4.43 r_work: 0.2763 rms_B_bonded: 4.97 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.1729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4786 Z= 0.225 Angle : 0.622 8.084 6427 Z= 0.328 Chirality : 0.041 0.130 679 Planarity : 0.003 0.048 859 Dihedral : 4.981 26.165 640 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.79 % Allowed : 12.67 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.35), residues: 594 helix: 2.49 (0.28), residues: 300 sheet: -1.09 (0.56), residues: 80 loop : -2.25 (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 50 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 46 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8523 (mpp) cc_final: 0.8116 (mpp) REVERT: A 203 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8339 (mtp) REVERT: A 207 ASP cc_start: 0.9216 (m-30) cc_final: 0.8995 (m-30) REVERT: B 187 TYR cc_start: 0.8981 (t80) cc_final: 0.8744 (t80) REVERT: B 282 PHE cc_start: 0.9326 (m-80) cc_final: 0.9051 (m-80) outliers start: 4 outliers final: 2 residues processed: 47 average time/residue: 0.1893 time to fit residues: 11.5667 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 : 0.523 ------------------------------------------------------------------------------- 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: 2.9990 chunk 29 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 57 optimal weight: 2.9990 chunk 21 optimal weight: 0.0770 chunk 48 optimal weight: 0.8980 overall best weight: 1.3142 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.057183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.042328 restraints weight = 20532.939| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.47 r_work: 0.2764 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4786 Z= 0.233 Angle : 0.621 8.189 6427 Z= 0.328 Chirality : 0.040 0.128 679 Planarity : 0.004 0.037 859 Dihedral : 4.889 25.381 640 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.58 % Allowed : 14.65 % Favored : 83.76 % 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: 0.61 (0.34), residues: 594 helix: 2.47 (0.28), residues: 301 sheet: -1.10 (0.55), residues: 79 loop : -2.15 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 184 HIS 0.001 0.001 HIS A 301 PHE 0.015 0.001 PHE B 136 TYR 0.013 0.001 TYR B 245 ARG 0.005 0.001 ARG B 275 *********************** 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: 8 poor density : 45 time to evaluate : 0.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8638 (mpp) cc_final: 0.8428 (mpp) REVERT: A 203 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.8196 (ttp) REVERT: A 207 ASP cc_start: 0.9242 (m-30) cc_final: 0.9017 (m-30) REVERT: B 187 TYR cc_start: 0.9009 (t80) cc_final: 0.8751 (t80) REVERT: B 282 PHE cc_start: 0.9357 (m-80) cc_final: 0.9038 (m-80) outliers start: 8 outliers final: 3 residues processed: 50 average time/residue: 0.1633 time to fit residues: 11.0924 Evaluate side-chains 43 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.556 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain B residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 58 random chunks: chunk 56 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- 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 = 0.3384 r_free = 0.3384 target = 0.057324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.042242 restraints weight = 20710.154| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 4.57 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4786 Z= 0.241 Angle : 0.612 7.732 6427 Z= 0.325 Chirality : 0.040 0.137 679 Planarity : 0.004 0.032 859 Dihedral : 4.859 24.956 640 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 15.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.58 % Allowed : 15.84 % 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: 0.63 (0.35), residues: 594 helix: 2.46 (0.28), residues: 301 sheet: -1.19 (0.55), residues: 79 loop : -2.06 (0.40), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 184 HIS 0.001 0.001 HIS A 301 PHE 0.015 0.001 PHE B 136 TYR 0.021 0.001 TYR A 158 ARG 0.005 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 54 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8288 (OUTLIER) cc_final: 0.7718 (ttp) REVERT: A 207 ASP cc_start: 0.8721 (m-30) cc_final: 0.8369 (m-30) REVERT: A 212 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: B 282 PHE cc_start: 0.9167 (m-80) cc_final: 0.8735 (m-80) outliers start: 8 outliers final: 4 residues processed: 51 average time/residue: 0.1476 time to fit residues: 10.2692 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 : 0.552 ------------------------------------------------------------------------------- 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 272 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 57 optimal weight: 0.6980 chunk 44 optimal weight: 0.0980 chunk 39 optimal weight: 0.9980 chunk 53 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.058011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.043232 restraints weight = 20488.944| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.50 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2468 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= 0.171 Angle : 0.603 7.716 6427 Z= 0.316 Chirality : 0.040 0.130 679 Planarity : 0.003 0.032 859 Dihedral : 4.694 23.836 640 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 13.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 1.19 % Allowed : 17.23 % Favored : 81.58 % 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: 0.76 (0.35), residues: 594 helix: 2.55 (0.28), residues: 301 sheet: -1.25 (0.55), residues: 79 loop : -1.91 (0.41), residues: 214 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 0.013 0.001 PHE B 136 TYR 0.018 0.001 TYR A 158 ARG 0.006 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 54 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7666 (ttp) REVERT: A 207 ASP cc_start: 0.8736 (m-30) cc_final: 0.8333 (m-30) REVERT: B 282 PHE cc_start: 0.9249 (m-80) cc_final: 0.8804 (m-80) outliers start: 6 outliers final: 5 residues processed: 51 average time/residue: 0.1808 time to fit residues: 12.0409 Evaluate side-chains 50 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.553 ------------------------------------------------------------------------------- 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 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: 0.0570 chunk 17 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.058488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.043853 restraints weight = 20176.755| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 4.48 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4786 Z= 0.159 Angle : 0.606 7.759 6427 Z= 0.314 Chirality : 0.040 0.130 679 Planarity : 0.003 0.032 859 Dihedral : 4.514 22.653 640 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.39 % Allowed : 17.43 % Favored : 81.19 % 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: 0.85 (0.35), residues: 594 helix: 2.60 (0.28), residues: 301 sheet: -1.22 (0.55), residues: 79 loop : -1.81 (0.41), residues: 214 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 0.015 0.001 TYR A 158 ARG 0.007 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 53 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8259 (OUTLIER) cc_final: 0.7742 (ttp) REVERT: A 207 ASP cc_start: 0.8737 (m-30) cc_final: 0.8352 (m-30) REVERT: B 38 MET cc_start: 0.8547 (mmm) cc_final: 0.7939 (mmm) REVERT: B 282 PHE cc_start: 0.9220 (m-80) cc_final: 0.8763 (m-80) outliers start: 7 outliers final: 5 residues processed: 50 average time/residue: 0.1495 time to fit residues: 10.2704 Evaluate side-chains 49 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 0 optimal weight: 8.9990 chunk 43 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 39 optimal weight: 0.4980 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 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 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 = 0.3417 r_free = 0.3417 target = 0.058351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.043648 restraints weight = 20325.525| |-----------------------------------------------------------------------------| r_work (start): 0.2980 rms_B_bonded: 4.49 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4786 Z= 0.174 Angle : 0.605 8.078 6427 Z= 0.314 Chirality : 0.040 0.132 679 Planarity : 0.003 0.029 859 Dihedral : 4.464 22.274 640 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.58 % Allowed : 17.43 % Favored : 80.99 % 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: 0.88 (0.35), residues: 594 helix: 2.60 (0.28), residues: 301 sheet: -1.19 (0.55), residues: 79 loop : -1.76 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 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 0.007 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 53 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 45 time to evaluate : 0.520 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8328 (OUTLIER) cc_final: 0.7635 (mtp) REVERT: A 207 ASP cc_start: 0.8760 (m-30) cc_final: 0.8373 (m-30) REVERT: B 38 MET cc_start: 0.8772 (mmm) cc_final: 0.8227 (mmm) REVERT: B 282 PHE cc_start: 0.9206 (m-80) cc_final: 0.8749 (m-80) outliers start: 8 outliers final: 6 residues processed: 50 average time/residue: 0.1639 time to fit residues: 11.0326 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 : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 3.9990 chunk 45 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 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 = 0.3418 r_free = 0.3418 target = 0.058506 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 = 20355.137| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 4.46 r_work: 0.2815 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.2903 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= 0.175 Angle : 0.619 8.787 6427 Z= 0.319 Chirality : 0.040 0.133 679 Planarity : 0.003 0.030 859 Dihedral : 4.410 21.755 640 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.58 % Allowed : 17.23 % Favored : 81.19 % 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: 0.90 (0.35), residues: 594 helix: 2.56 (0.28), residues: 303 sheet: -1.19 (0.55), residues: 79 loop : -1.72 (0.41), residues: 212 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 0.014 0.001 TYR A 158 ARG 0.007 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 54 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 203 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8479 (ttm) REVERT: A 207 ASP cc_start: 0.9303 (m-30) cc_final: 0.8939 (m-30) REVERT: B 216 TYR cc_start: 0.9211 (m-10) cc_final: 0.8988 (m-10) REVERT: B 282 PHE cc_start: 0.9292 (m-80) cc_final: 0.8944 (m-80) outliers start: 8 outliers final: 6 residues processed: 51 average time/residue: 0.1679 time to fit residues: 11.4760 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 : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 0.9980 chunk 22 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 14 optimal weight: 0.3980 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 = 0.3425 r_free = 0.3425 target = 0.058748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.043995 restraints weight = 20025.437| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 4.46 r_work: 0.2822 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2989 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= 0.171 Angle : 0.623 9.315 6427 Z= 0.321 Chirality : 0.040 0.135 679 Planarity : 0.003 0.029 859 Dihedral : 4.372 21.309 640 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 1.78 % Allowed : 17.62 % 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: 0.88 (0.35), residues: 594 helix: 2.51 (0.28), residues: 304 sheet: -1.14 (0.56), residues: 79 loop : -1.71 (0.41), residues: 211 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 0.014 0.001 TYR A 158 ARG 0.007 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 : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.8178 (mpp) cc_final: 0.7591 (pmm) REVERT: A 203 MET cc_start: 0.8722 (OUTLIER) cc_final: 0.8204 (mtp) REVERT: A 207 ASP cc_start: 0.9312 (m-30) cc_final: 0.8979 (m-30) REVERT: B 216 TYR cc_start: 0.9162 (m-10) cc_final: 0.8927 (m-10) REVERT: B 282 PHE cc_start: 0.9307 (m-80) cc_final: 0.8956 (m-80) outliers start: 9 outliers final: 6 residues processed: 51 average time/residue: 0.1395 time to fit residues: 9.9168 Evaluate side-chains 51 residues out of total 505 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 44 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 38 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.058111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.043453 restraints weight = 20201.776| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 4.42 r_work: 0.2803 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4786 Z= 0.202 Angle : 0.641 9.473 6427 Z= 0.328 Chirality : 0.041 0.157 679 Planarity : 0.003 0.027 859 Dihedral : 4.423 21.379 640 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.58 % Allowed : 18.42 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.34), residues: 594 helix: 2.47 (0.28), residues: 304 sheet: -1.13 (0.56), residues: 79 loop : -1.77 (0.40), residues: 211 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 0.013 0.001 TYR B 245 ARG 0.007 0.001 ARG B 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2119.24 seconds wall clock time: 37 minutes 24.99 seconds (2244.99 seconds total)