Starting phenix.real_space_refine on Mon Aug 25 16:38:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h3l_0135/08_2025/6h3l_0135.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h3l_0135/08_2025/6h3l_0135.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6h3l_0135/08_2025/6h3l_0135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h3l_0135/08_2025/6h3l_0135.map" model { file = "/net/cci-nas-00/data/ceres_data/6h3l_0135/08_2025/6h3l_0135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h3l_0135/08_2025/6h3l_0135.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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: 5 Type Number sf(0) Gaussians S 45 5.16 5 C 9339 2.51 5 N 2730 2.21 5 O 2817 1.98 5 H 14388 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 73 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29319 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 591} Chain breaks: 1 Chain: "B" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 31, 'TRANS': 591} Chain breaks: 1 Chain: "C" Number of atoms: 9773 Number of conformers: 1 Conformer: "" Number of residues, atoms: 627, 9773 Classifications: {'peptide': 627} Link IDs: {'CIS': 1, 'PCIS': 2, 'PTRANS': 32, 'TRANS': 591} Chain breaks: 1 Time building chain proxies: 5.38, per 1000 atoms: 0.18 Number of scatterers: 29319 At special positions: 0 Unit cell: (90.06, 91.2, 183.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 O 2817 8.00 N 2730 7.00 C 9339 6.00 H 14388 1.00 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: 3.30 Conformation dependent library (CDL) restraints added in 981.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 0 sheets defined 14.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'A' and resid 14 through 16 No H-bonds generated for 'chain 'A' and resid 14 through 16' Processing helix chain 'A' and resid 63 through 65 No H-bonds generated for 'chain 'A' and resid 63 through 65' Processing helix chain 'A' and resid 95 through 102 Processing helix chain 'A' and resid 114 through 126 Processing helix chain 'A' and resid 151 through 161 Processing helix chain 'A' and resid 182 through 186 Processing helix chain 'A' and resid 199 through 203 Processing helix chain 'A' and resid 264 through 283 removed outlier: 4.426A pdb=" N ALA A 278 " --> pdb=" O ASN A 274 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N HIS A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 312 Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 626 through 637 Processing helix chain 'B' and resid 47 through 51 Processing helix chain 'B' and resid 63 through 65 No H-bonds generated for 'chain 'B' and resid 63 through 65' Processing helix chain 'B' and resid 95 through 102 Processing helix chain 'B' and resid 114 through 126 Processing helix chain 'B' and resid 151 through 163 Processing helix chain 'B' and resid 182 through 186 Processing helix chain 'B' and resid 199 through 203 Processing helix chain 'B' and resid 264 through 281 Processing helix chain 'B' and resid 308 through 312 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 625 through 637 Processing helix chain 'C' and resid 47 through 51 Processing helix chain 'C' and resid 63 through 65 No H-bonds generated for 'chain 'C' and resid 63 through 65' Processing helix chain 'C' and resid 95 through 102 Processing helix chain 'C' and resid 113 through 126 Processing helix chain 'C' and resid 151 through 163 Processing helix chain 'C' and resid 182 through 186 Processing helix chain 'C' and resid 199 through 203 Processing helix chain 'C' and resid 264 through 281 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 625 through 637 156 hydrogen bonds defined for protein. 363 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: 8.29 Time building geometry restraints manager: 4.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 14367 1.13 - 1.30: 2552 1.30 - 1.47: 6361 1.47 - 1.64: 6324 1.64 - 1.81: 69 Bond restraints: 29673 Sorted by residual: bond pdb=" N HIS C 393 " pdb=" H HIS C 393 " ideal model delta sigma weight residual 0.860 1.023 -0.163 2.00e-02 2.50e+03 6.68e+01 bond pdb=" CE1 HIS B 170 " pdb=" HE1 HIS B 170 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.56e+01 bond pdb=" CE1 TYR C 458 " pdb=" HE1 TYR C 458 " ideal model delta sigma weight residual 0.930 1.092 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" N PHE C 592 " pdb=" H PHE C 592 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" N THR C 150 " pdb=" H THR C 150 " ideal model delta sigma weight residual 0.860 1.021 -0.161 2.00e-02 2.50e+03 6.52e+01 ... (remaining 29668 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 47196 2.79 - 5.58: 4639 5.58 - 8.38: 1393 8.38 - 11.17: 61 11.17 - 13.96: 24 Bond angle restraints: 53313 Sorted by residual: angle pdb=" C PRO B 638 " pdb=" N PRO B 639 " pdb=" CA PRO B 639 " ideal model delta sigma weight residual 119.66 127.18 -7.52 7.20e-01 1.93e+00 1.09e+02 angle pdb=" N CYS A 11 " pdb=" CA CYS A 11 " pdb=" C CYS A 11 " ideal model delta sigma weight residual 108.07 116.96 -8.89 8.90e-01 1.26e+00 9.97e+01 angle pdb=" C PRO C 638 " pdb=" N PRO C 639 " pdb=" CA PRO C 639 " ideal model delta sigma weight residual 119.66 126.77 -7.11 7.20e-01 1.93e+00 9.76e+01 angle pdb=" C PHE A 637 " pdb=" N PRO A 638 " pdb=" CA PRO A 638 " ideal model delta sigma weight residual 119.66 126.62 -6.96 7.20e-01 1.93e+00 9.36e+01 angle pdb=" C PRO B 199 " pdb=" N PRO B 200 " pdb=" CA PRO B 200 " ideal model delta sigma weight residual 119.56 128.78 -9.22 1.01e+00 9.80e-01 8.34e+01 ... (remaining 53308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 13191 17.98 - 35.96: 526 35.96 - 53.94: 196 53.94 - 71.92: 80 71.92 - 89.90: 23 Dihedral angle restraints: 14016 sinusoidal: 7665 harmonic: 6351 Sorted by residual: dihedral pdb=" CD2 HIS B 209 " pdb=" CG HIS B 209 " pdb=" ND1 HIS B 209 " pdb=" HD1 HIS B 209 " ideal model delta harmonic sigma weight residual -180.00 -145.76 -34.24 0 5.00e+00 4.00e-02 4.69e+01 dihedral pdb=" CD2 HIS A 204 " pdb=" CG HIS A 204 " pdb=" ND1 HIS A 204 " pdb=" HD1 HIS A 204 " ideal model delta harmonic sigma weight residual 180.00 -146.83 -33.17 0 5.00e+00 4.00e-02 4.40e+01 dihedral pdb=" CD2 HIS A 71 " pdb=" CG HIS A 71 " pdb=" ND1 HIS A 71 " pdb=" HD1 HIS A 71 " ideal model delta harmonic sigma weight residual 180.00 -148.02 -31.98 0 5.00e+00 4.00e-02 4.09e+01 ... (remaining 14013 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1195 0.065 - 0.131: 703 0.131 - 0.196: 217 0.196 - 0.261: 24 0.261 - 0.326: 3 Chirality restraints: 2142 Sorted by residual: chirality pdb=" CA PRO C 97 " pdb=" N PRO C 97 " pdb=" C PRO C 97 " pdb=" CB PRO C 97 " both_signs ideal model delta sigma weight residual False 2.72 2.39 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CA PRO A 196 " pdb=" N PRO A 196 " pdb=" C PRO A 196 " pdb=" CB PRO A 196 " both_signs ideal model delta sigma weight residual False 2.72 2.45 0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" CA SER A 588 " pdb=" N SER A 588 " pdb=" C SER A 588 " pdb=" CB SER A 588 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 2139 not shown) Planarity restraints: 4569 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 71 " 0.140 2.00e-02 2.50e+03 1.26e-01 3.55e+02 pdb=" CG HIS A 71 " 0.044 2.00e-02 2.50e+03 pdb=" ND1 HIS A 71 " 0.103 2.00e-02 2.50e+03 pdb=" CD2 HIS A 71 " -0.040 2.00e-02 2.50e+03 pdb=" CE1 HIS A 71 " 0.065 2.00e-02 2.50e+03 pdb=" NE2 HIS A 71 " -0.032 2.00e-02 2.50e+03 pdb=" HD1 HIS A 71 " -0.291 2.00e-02 2.50e+03 pdb=" HD2 HIS A 71 " -0.090 2.00e-02 2.50e+03 pdb=" HE1 HIS A 71 " 0.101 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 209 " -0.112 2.00e-02 2.50e+03 1.23e-01 3.39e+02 pdb=" CG HIS B 209 " -0.057 2.00e-02 2.50e+03 pdb=" ND1 HIS B 209 " -0.118 2.00e-02 2.50e+03 pdb=" CD2 HIS B 209 " 0.028 2.00e-02 2.50e+03 pdb=" CE1 HIS B 209 " -0.065 2.00e-02 2.50e+03 pdb=" NE2 HIS B 209 " 0.039 2.00e-02 2.50e+03 pdb=" HD1 HIS B 209 " 0.286 2.00e-02 2.50e+03 pdb=" HD2 HIS B 209 " 0.092 2.00e-02 2.50e+03 pdb=" HE1 HIS B 209 " -0.095 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 175 " 0.148 2.00e-02 2.50e+03 1.21e-01 3.31e+02 pdb=" CG HIS B 175 " 0.029 2.00e-02 2.50e+03 pdb=" ND1 HIS B 175 " 0.087 2.00e-02 2.50e+03 pdb=" CD2 HIS B 175 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 HIS B 175 " 0.061 2.00e-02 2.50e+03 pdb=" NE2 HIS B 175 " -0.023 2.00e-02 2.50e+03 pdb=" HD1 HIS B 175 " -0.277 2.00e-02 2.50e+03 pdb=" HD2 HIS B 175 " -0.086 2.00e-02 2.50e+03 pdb=" HE1 HIS B 175 " 0.107 2.00e-02 2.50e+03 ... (remaining 4566 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.98: 1698 1.98 - 2.64: 39196 2.64 - 3.29: 97559 3.29 - 3.95: 132567 3.95 - 4.60: 199254 Nonbonded interactions: 470274 Sorted by model distance: nonbonded pdb=" OE1 GLU C 494 " pdb=" H GLU C 494 " model vdw 1.330 2.450 nonbonded pdb=" OE1 GLU A 142 " pdb=" H GLU A 142 " model vdw 1.361 2.450 nonbonded pdb=" OE1 GLU A 459 " pdb=" H GLU A 459 " model vdw 1.388 2.450 nonbonded pdb=" OE1 GLU B 206 " pdb=" H GLU B 206 " model vdw 1.402 2.450 nonbonded pdb=" OE1 GLU A 49 " pdb=" H GLU A 49 " model vdw 1.406 2.450 ... (remaining 470269 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 group one per residue 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: 2.860 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: 0.100 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 31.920 Find NCS groups from input model: 0.690 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:1.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 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 : 0.015 0.065 15285 Z= 0.965 Angle : 1.697 12.873 20715 Z= 1.151 Chirality : 0.082 0.326 2142 Planarity : 0.011 0.137 2796 Dihedral : 11.552 89.900 5700 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.91 % Allowed : 7.65 % Favored : 91.44 % Rotamer: Outliers : 0.06 % Allowed : 0.57 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.43 (0.18), residues: 1869 helix: 0.29 (0.35), residues: 174 sheet: -1.01 (0.22), residues: 489 loop : -1.12 (0.17), residues: 1206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 76 TYR 0.076 0.009 TYR A 306 PHE 0.031 0.006 PHE A 33 TRP 0.061 0.008 TRP A 419 HIS 0.014 0.002 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.01538 (15285) covalent geometry : angle 1.69713 (20715) hydrogen bonds : bond 0.13947 ( 156) hydrogen bonds : angle 5.81347 ( 363) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.887 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 359 THR cc_start: 0.4743 (m) cc_final: 0.4185 (p) REVERT: B 364 VAL cc_start: 0.6797 (t) cc_final: 0.5306 (t) REVERT: C 159 MET cc_start: 0.8382 (ttp) cc_final: 0.8136 (tmm) REVERT: C 422 MET cc_start: 0.5597 (tmm) cc_final: 0.5359 (tmm) outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.3653 time to fit residues: 39.4772 Evaluate side-chains 52 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 264 GLN A 358 GLN ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 214 GLN ** C 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.033777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.029640 restraints weight = 547721.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.030514 restraints weight = 353908.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.031130 restraints weight = 245213.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.031549 restraints weight = 179158.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.031821 restraints weight = 136604.971| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 15285 Z= 0.297 Angle : 0.736 6.012 20715 Z= 0.413 Chirality : 0.046 0.184 2142 Planarity : 0.008 0.080 2796 Dihedral : 5.436 21.909 2109 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.03 % Favored : 94.70 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.73 (0.18), residues: 1869 helix: -0.11 (0.36), residues: 180 sheet: -1.52 (0.22), residues: 516 loop : -1.12 (0.17), residues: 1173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 409 TYR 0.026 0.002 TYR C 271 PHE 0.035 0.003 PHE B 122 TRP 0.016 0.002 TRP B 414 HIS 0.010 0.002 HIS A 526 Details of bonding type rmsd covalent geometry : bond 0.00620 (15285) covalent geometry : angle 0.73571 (20715) hydrogen bonds : bond 0.05703 ( 156) hydrogen bonds : angle 5.29556 ( 363) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 159 MET cc_start: 0.8633 (ttp) cc_final: 0.8354 (tmm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.3470 time to fit residues: 28.1082 Evaluate side-chains 46 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 104 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 8 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 173 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 19 optimal weight: 8.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 214 GLN A 232 GLN B 264 GLN B 326 GLN B 358 GLN B 423 GLN C 270 GLN C 274 ASN C 358 GLN C 463 ASN ** C 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.032533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.028613 restraints weight = 583573.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.029383 restraints weight = 383288.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.029947 restraints weight = 269164.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.030326 restraints weight = 198104.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.030571 restraints weight = 151952.821| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 15285 Z= 0.305 Angle : 0.702 5.785 20715 Z= 0.393 Chirality : 0.044 0.183 2142 Planarity : 0.007 0.069 2796 Dihedral : 5.378 23.264 2109 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.44 % Favored : 92.40 % Rotamer: Outliers : 0.06 % Allowed : 0.82 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.18), residues: 1869 helix: -0.11 (0.37), residues: 180 sheet: -2.00 (0.22), residues: 525 loop : -1.43 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 409 TYR 0.030 0.003 TYR B 258 PHE 0.031 0.003 PHE B 301 TRP 0.014 0.002 TRP B 414 HIS 0.008 0.002 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00599 (15285) covalent geometry : angle 0.70204 (20715) hydrogen bonds : bond 0.05161 ( 156) hydrogen bonds : angle 5.35754 ( 363) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 48 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8475 (tmm) cc_final: 0.8252 (tmm) outliers start: 1 outliers final: 0 residues processed: 49 average time/residue: 0.3602 time to fit residues: 26.1239 Evaluate side-chains 43 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 9 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 100 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 142 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN B 21 GLN ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.032042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.028088 restraints weight = 582542.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.028872 restraints weight = 380971.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.029409 restraints weight = 266201.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.029785 restraints weight = 197935.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.030039 restraints weight = 152544.403| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.3505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 15285 Z= 0.248 Angle : 0.637 6.550 20715 Z= 0.352 Chirality : 0.044 0.166 2142 Planarity : 0.006 0.058 2796 Dihedral : 5.427 23.943 2109 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.12 % Favored : 92.72 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.18), residues: 1869 helix: 0.17 (0.38), residues: 183 sheet: -2.23 (0.21), residues: 555 loop : -1.65 (0.17), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 76 TYR 0.021 0.002 TYR C 271 PHE 0.023 0.002 PHE B 301 TRP 0.032 0.002 TRP A 213 HIS 0.007 0.002 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00499 (15285) covalent geometry : angle 0.63717 (20715) hydrogen bonds : bond 0.04518 ( 156) hydrogen bonds : angle 5.14560 ( 363) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 392 PHE cc_start: 0.9052 (m-80) cc_final: 0.8781 (m-80) REVERT: C 487 MET cc_start: 0.8671 (mtt) cc_final: 0.8356 (mtt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2756 time to fit residues: 18.7648 Evaluate side-chains 37 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 88 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 53 optimal weight: 8.9990 chunk 65 optimal weight: 9.9990 chunk 90 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 62 optimal weight: 10.0000 chunk 102 optimal weight: 0.7980 chunk 77 optimal weight: 4.9990 chunk 181 optimal weight: 9.9990 chunk 120 optimal weight: 0.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN B 506 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.032277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.028061 restraints weight = 578622.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.028889 restraints weight = 381671.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.029481 restraints weight = 266612.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.029805 restraints weight = 196763.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.030133 restraints weight = 159963.000| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15285 Z= 0.184 Angle : 0.569 4.307 20715 Z= 0.310 Chirality : 0.043 0.165 2142 Planarity : 0.005 0.053 2796 Dihedral : 5.191 23.346 2109 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.49 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.18), residues: 1869 helix: 0.50 (0.38), residues: 183 sheet: -2.34 (0.21), residues: 546 loop : -1.58 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 486 TYR 0.017 0.002 TYR C 271 PHE 0.027 0.002 PHE C 392 TRP 0.016 0.002 TRP A 213 HIS 0.006 0.001 HIS A 71 Details of bonding type rmsd covalent geometry : bond 0.00374 (15285) covalent geometry : angle 0.56867 (20715) hydrogen bonds : bond 0.04253 ( 156) hydrogen bonds : angle 4.92675 ( 363) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 469 MET cc_start: 0.7265 (ppp) cc_final: 0.7052 (ppp) REVERT: C 344 LEU cc_start: 0.8825 (mt) cc_final: 0.8478 (mt) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.3047 time to fit residues: 20.6462 Evaluate side-chains 35 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 99 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 37 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 chunk 116 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 96 optimal weight: 0.3980 chunk 32 optimal weight: 5.9990 chunk 43 optimal weight: 5.9990 chunk 121 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 overall best weight: 2.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 ASN C 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.032092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.027967 restraints weight = 580572.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.028777 restraints weight = 378547.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.029352 restraints weight = 264396.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.029765 restraints weight = 196331.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.030017 restraints weight = 150824.646| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 15285 Z= 0.184 Angle : 0.558 4.581 20715 Z= 0.304 Chirality : 0.043 0.161 2142 Planarity : 0.005 0.054 2796 Dihedral : 5.116 23.364 2109 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.22 % Favored : 92.67 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.42 (0.19), residues: 1869 helix: 0.55 (0.38), residues: 183 sheet: -2.40 (0.21), residues: 546 loop : -1.55 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 486 TYR 0.017 0.002 TYR C 271 PHE 0.022 0.002 PHE C 168 TRP 0.016 0.002 TRP B 167 HIS 0.010 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00374 (15285) covalent geometry : angle 0.55787 (20715) hydrogen bonds : bond 0.04125 ( 156) hydrogen bonds : angle 4.83833 ( 363) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 344 LEU cc_start: 0.8678 (mt) cc_final: 0.8354 (mt) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.3085 time to fit residues: 20.3581 Evaluate side-chains 35 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 53 optimal weight: 7.9990 chunk 116 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 156 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 506 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.032274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.027912 restraints weight = 567800.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.028774 restraints weight = 368551.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.029391 restraints weight = 256777.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.029842 restraints weight = 188661.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.030138 restraints weight = 144570.565| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15285 Z= 0.129 Angle : 0.519 9.283 20715 Z= 0.278 Chirality : 0.043 0.157 2142 Planarity : 0.005 0.051 2796 Dihedral : 4.921 22.478 2109 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.90 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.19), residues: 1869 helix: 0.81 (0.39), residues: 183 sheet: -2.33 (0.22), residues: 534 loop : -1.47 (0.17), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 538 TYR 0.012 0.001 TYR C 271 PHE 0.013 0.001 PHE B 301 TRP 0.010 0.001 TRP A 213 HIS 0.006 0.001 HIS C 175 Details of bonding type rmsd covalent geometry : bond 0.00267 (15285) covalent geometry : angle 0.51893 (20715) hydrogen bonds : bond 0.03902 ( 156) hydrogen bonds : angle 4.63382 ( 363) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.862 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 159 MET cc_start: 0.8703 (mtp) cc_final: 0.8361 (mmm) REVERT: C 344 LEU cc_start: 0.8567 (mt) cc_final: 0.8249 (mt) REVERT: C 422 MET cc_start: 0.4504 (tmm) cc_final: 0.4217 (tmm) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.3137 time to fit residues: 20.1543 Evaluate side-chains 36 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 162 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 100 optimal weight: 8.9990 chunk 181 optimal weight: 9.9990 chunk 101 optimal weight: 7.9990 chunk 75 optimal weight: 6.9990 chunk 151 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 174 optimal weight: 5.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 270 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 626 GLN ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 GLN ** B 391 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 399 GLN ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 601 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.030849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.026740 restraints weight = 626221.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.027511 restraints weight = 404066.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.028056 restraints weight = 278659.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.028447 restraints weight = 204753.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.028738 restraints weight = 159208.326| |-----------------------------------------------------------------------------| r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.096 15285 Z= 0.411 Angle : 0.810 6.753 20715 Z= 0.447 Chirality : 0.046 0.208 2142 Planarity : 0.007 0.074 2796 Dihedral : 5.802 26.327 2109 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 27.36 Ramachandran Plot: Outliers : 0.27 % Allowed : 11.99 % Favored : 87.75 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.40 (0.18), residues: 1869 helix: -0.57 (0.35), residues: 183 sheet: -2.84 (0.20), residues: 543 loop : -2.30 (0.16), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 486 TYR 0.034 0.003 TYR C 271 PHE 0.063 0.004 PHE C 86 TRP 0.019 0.003 TRP C 407 HIS 0.013 0.002 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00830 (15285) covalent geometry : angle 0.81040 (20715) hydrogen bonds : bond 0.04953 ( 156) hydrogen bonds : angle 5.79390 ( 363) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8839 (tmm) cc_final: 0.8593 (tmm) REVERT: C 344 LEU cc_start: 0.9063 (mt) cc_final: 0.8848 (mt) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2845 time to fit residues: 15.9599 Evaluate side-chains 31 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 18 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 184 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN A 274 ASN B 90 GLN B 391 HIS ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.031437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.027393 restraints weight = 586538.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.028170 restraints weight = 382334.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.028705 restraints weight = 266970.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.029122 restraints weight = 199049.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.029415 restraints weight = 153491.115| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15285 Z= 0.161 Angle : 0.572 5.008 20715 Z= 0.309 Chirality : 0.044 0.168 2142 Planarity : 0.006 0.056 2796 Dihedral : 5.343 22.635 2109 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.40 % Favored : 91.49 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.93 (0.18), residues: 1869 helix: 0.07 (0.37), residues: 183 sheet: -2.72 (0.20), residues: 567 loop : -1.87 (0.17), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 323 TYR 0.016 0.002 TYR C 271 PHE 0.020 0.002 PHE C 86 TRP 0.017 0.002 TRP C 98 HIS 0.007 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00330 (15285) covalent geometry : angle 0.57223 (20715) hydrogen bonds : bond 0.04050 ( 156) hydrogen bonds : angle 4.86527 ( 363) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 23 MET cc_start: 0.8879 (tmm) cc_final: 0.8678 (tmm) REVERT: A 215 MET cc_start: 0.5924 (ppp) cc_final: 0.5684 (ppp) REVERT: B 159 MET cc_start: 0.8845 (mtp) cc_final: 0.8511 (mmm) REVERT: C 422 MET cc_start: 0.4906 (tmm) cc_final: 0.4594 (tmm) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2491 time to fit residues: 14.9435 Evaluate side-chains 28 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 133 optimal weight: 6.9990 chunk 104 optimal weight: 5.9990 chunk 95 optimal weight: 10.0000 chunk 153 optimal weight: 3.9990 chunk 32 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 174 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 68 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 274 ASN ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 124 ASN B 506 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.031469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.027355 restraints weight = 583848.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.028135 restraints weight = 381321.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.028696 restraints weight = 267833.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.029094 restraints weight = 198970.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.029389 restraints weight = 154656.907| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.4850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15285 Z= 0.142 Angle : 0.534 5.086 20715 Z= 0.286 Chirality : 0.043 0.220 2142 Planarity : 0.005 0.052 2796 Dihedral : 5.002 21.401 2109 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.51 % Favored : 91.39 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.62 (0.19), residues: 1869 helix: 0.61 (0.38), residues: 183 sheet: -2.61 (0.21), residues: 537 loop : -1.70 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 187 TYR 0.012 0.001 TYR B 322 PHE 0.016 0.002 PHE C 168 TRP 0.012 0.001 TRP C 98 HIS 0.006 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00300 (15285) covalent geometry : angle 0.53413 (20715) hydrogen bonds : bond 0.03866 ( 156) hydrogen bonds : angle 4.62151 ( 363) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3738 Ramachandran restraints generated. 1869 Oldfield, 0 Emsley, 1869 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 MET cc_start: 0.5944 (ppp) cc_final: 0.5712 (ppp) REVERT: B 159 MET cc_start: 0.8758 (mtp) cc_final: 0.8421 (mmm) REVERT: C 422 MET cc_start: 0.4805 (tmm) cc_final: 0.4476 (tmm) outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.2146 time to fit residues: 13.2196 Evaluate side-chains 31 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 48 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 179 optimal weight: 1.9990 chunk 185 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 141 optimal weight: 0.1980 chunk 24 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 43 optimal weight: 2.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 495 GLN ** 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 = 0.3562 r_free = 0.3562 target = 0.031570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.027412 restraints weight = 585000.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.028194 restraints weight = 383845.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.028767 restraints weight = 270007.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.029190 restraints weight = 199535.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.029474 restraints weight = 154024.754| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15285 Z= 0.126 Angle : 0.517 4.963 20715 Z= 0.276 Chirality : 0.043 0.155 2142 Planarity : 0.005 0.052 2796 Dihedral : 4.896 21.184 2109 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.52 (0.19), residues: 1869 helix: 0.71 (0.38), residues: 183 sheet: -2.61 (0.20), residues: 573 loop : -1.54 (0.18), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 187 TYR 0.011 0.001 TYR B 322 PHE 0.014 0.002 PHE C 168 TRP 0.010 0.001 TRP A 213 HIS 0.005 0.001 HIS C 170 Details of bonding type rmsd covalent geometry : bond 0.00269 (15285) covalent geometry : angle 0.51682 (20715) hydrogen bonds : bond 0.03937 ( 156) hydrogen bonds : angle 4.58300 ( 363) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4076.44 seconds wall clock time: 70 minutes 52.71 seconds (4252.71 seconds total)