Starting phenix.real_space_refine on Wed Jun 25 09:05:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6h3l_0135/06_2025/6h3l_0135.cif Found real_map, /net/cci-nas-00/data/ceres_data/6h3l_0135/06_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_0135/06_2025/6h3l_0135.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6h3l_0135/06_2025/6h3l_0135.map" model { file = "/net/cci-nas-00/data/ceres_data/6h3l_0135/06_2025/6h3l_0135.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6h3l_0135/06_2025/6h3l_0135.cif" } resolution = 4.2 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= 0.003 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.98, per 1000 atoms: 0.48 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: 7.48 Conformation dependent library (CDL) restraints added in 2.3 seconds 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: 1.72 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: 9.44 Time building geometry restraints manager: 9.11 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: 0.00 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: 38.880 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: 0.510 Extract box with map and model: 1.120 Check model and map are aligned: 0.210 Set scattering table: 0.270 Process input model: 58.600 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.090 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 103.220 ------------------------------------------------------------------------------- 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 (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: -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 TRP 0.061 0.008 TRP A 419 HIS 0.014 0.002 HIS A 526 PHE 0.031 0.006 PHE A 33 TYR 0.076 0.009 TYR A 306 ARG 0.006 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.13947 ( 156) hydrogen bonds : angle 5.81347 ( 363) covalent geometry : bond 0.01538 (15285) covalent geometry : angle 1.69713 (20715) *********************** 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 : 2.168 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: 0.5307 (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: 0.6645 time to fit residues: 72.6250 Evaluate side-chains 53 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 52 time to evaluate : 2.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 157 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 48 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 145 optimal weight: 6.9990 chunk 56 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 108 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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 391 HIS ** C 526 HIS ** 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 = 0.3645 r_free = 0.3645 target = 0.033282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.029279 restraints weight = 566717.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.030092 restraints weight = 372275.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.030678 restraints weight = 260068.644| |-----------------------------------------------------------------------------| r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.087 15285 Z= 0.363 Angle : 0.795 6.141 20715 Z= 0.448 Chirality : 0.047 0.190 2142 Planarity : 0.008 0.083 2796 Dihedral : 5.503 22.011 2109 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.51 % Favored : 94.22 % Rotamer: Outliers : 0.06 % Allowed : 1.08 % 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 (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: -1.88 (0.18), residues: 1869 helix: -0.31 (0.35), residues: 180 sheet: -1.64 (0.21), residues: 540 loop : -1.17 (0.17), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 414 HIS 0.011 0.003 HIS B 186 PHE 0.029 0.003 PHE C 301 TYR 0.028 0.002 TYR C 271 ARG 0.011 0.001 ARG A 409 Details of bonding type rmsd hydrogen bonds : bond 0.05995 ( 156) hydrogen bonds : angle 5.61576 ( 363) covalent geometry : bond 0.00745 (15285) covalent geometry : angle 0.79451 (20715) *********************** 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 56 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 2.153 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: C 159 MET cc_start: 0.8743 (ttp) cc_final: 0.8423 (tmm) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.6842 time to fit residues: 56.7901 Evaluate side-chains 45 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 2.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 74 optimal weight: 6.9990 chunk 161 optimal weight: 5.9990 chunk 125 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 155 optimal weight: 0.9990 chunk 70 optimal weight: 10.0000 chunk 71 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 114 optimal weight: 7.9990 chunk 178 optimal weight: 0.7980 chunk 38 optimal weight: 10.0000 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 326 GLN C 391 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.033881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.029849 restraints weight = 549402.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.030658 restraints weight = 365214.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.031246 restraints weight = 257903.980| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15285 Z= 0.159 Angle : 0.585 5.549 20715 Z= 0.323 Chirality : 0.044 0.170 2142 Planarity : 0.006 0.060 2796 Dihedral : 5.231 21.168 2109 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.67 % Favored : 94.17 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: -1.77 (0.19), residues: 1869 helix: 0.34 (0.37), residues: 180 sheet: -1.74 (0.22), residues: 522 loop : -1.12 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 414 HIS 0.007 0.001 HIS C 175 PHE 0.018 0.002 PHE C 301 TYR 0.019 0.002 TYR B 258 ARG 0.008 0.000 ARG B 409 Details of bonding type rmsd hydrogen bonds : bond 0.04986 ( 156) hydrogen bonds : angle 4.95489 ( 363) covalent geometry : bond 0.00315 (15285) covalent geometry : angle 0.58492 (20715) *********************** 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 51 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 2.305 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: A 388 VAL cc_start: 0.9073 (m) cc_final: 0.8840 (p) REVERT: B 392 PHE cc_start: 0.8994 (m-80) cc_final: 0.8697 (m-80) REVERT: C 159 MET cc_start: 0.8735 (ttp) cc_final: 0.8323 (tmm) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.6812 time to fit residues: 52.9230 Evaluate side-chains 47 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 2.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 16 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 89 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 1.9990 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 135 optimal weight: 4.9990 chunk 125 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 311 GLN B 264 GLN B 358 GLN C 270 GLN C 463 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.033402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.029425 restraints weight = 561798.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.030225 restraints weight = 373919.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.030770 restraints weight = 264446.770| |-----------------------------------------------------------------------------| r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15285 Z= 0.169 Angle : 0.557 5.076 20715 Z= 0.305 Chirality : 0.043 0.160 2142 Planarity : 0.005 0.053 2796 Dihedral : 5.070 26.040 2109 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.05 % Favored : 93.79 % 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 (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: -1.85 (0.19), residues: 1869 helix: 0.65 (0.38), residues: 180 sheet: -1.92 (0.21), residues: 540 loop : -1.16 (0.18), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 213 HIS 0.005 0.001 HIS C 391 PHE 0.018 0.002 PHE B 301 TYR 0.016 0.002 TYR C 271 ARG 0.005 0.000 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.04502 ( 156) hydrogen bonds : angle 4.81493 ( 363) covalent geometry : bond 0.00339 (15285) covalent geometry : angle 0.55689 (20715) *********************** 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 50 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 2.222 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: B 392 PHE cc_start: 0.8989 (m-80) cc_final: 0.8725 (m-80) REVERT: B 422 MET cc_start: 0.7885 (ppp) cc_final: 0.7590 (ppp) REVERT: C 487 MET cc_start: 0.8593 (mtt) cc_final: 0.8260 (mtt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.6754 time to fit residues: 51.3744 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 : 2.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 107 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 123 optimal weight: 5.9990 chunk 162 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 71 optimal weight: 0.2980 chunk 157 optimal weight: 10.0000 chunk 118 optimal weight: 3.9990 chunk 26 optimal weight: 10.0000 chunk 158 optimal weight: 0.6980 chunk 163 optimal weight: 6.9990 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 510 ASN B 21 GLN B 423 GLN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 HIS C 274 ASN C 358 GLN ** C 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.032234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.028251 restraints weight = 587218.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.029036 restraints weight = 384624.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.029574 restraints weight = 270256.212| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 15285 Z= 0.233 Angle : 0.620 5.514 20715 Z= 0.339 Chirality : 0.043 0.166 2142 Planarity : 0.006 0.059 2796 Dihedral : 5.132 24.948 2109 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.60 % Favored : 92.24 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: -2.30 (0.18), residues: 1869 helix: 0.55 (0.38), residues: 183 sheet: -2.20 (0.21), residues: 531 loop : -1.55 (0.17), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 213 HIS 0.006 0.002 HIS A 71 PHE 0.026 0.002 PHE B 168 TYR 0.025 0.002 TYR B 166 ARG 0.017 0.001 ARG B 607 Details of bonding type rmsd hydrogen bonds : bond 0.04319 ( 156) hydrogen bonds : angle 5.01591 ( 363) covalent geometry : bond 0.00473 (15285) covalent geometry : angle 0.61951 (20715) *********************** 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 49 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 2.316 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: A 23 MET cc_start: 0.8567 (tmm) cc_final: 0.8224 (tmm) REVERT: B 159 MET cc_start: 0.8881 (mtp) cc_final: 0.8472 (mmm) REVERT: C 487 MET cc_start: 0.8558 (mtt) cc_final: 0.8263 (mtp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.7555 time to fit residues: 54.6848 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 : 2.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 20 optimal weight: 10.0000 chunk 19 optimal weight: 0.7980 chunk 181 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 129 optimal weight: 10.0000 chunk 85 optimal weight: 0.0980 chunk 40 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 60 optimal weight: 6.9990 chunk 87 optimal weight: 1.9990 chunk 185 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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** B 506 ASN ** C 38 HIS ** 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 = 0.3609 r_free = 0.3609 target = 0.032589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.028270 restraints weight = 567377.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.029143 restraints weight = 366166.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.029764 restraints weight = 253511.477| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3667 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= 0.153 Angle : 0.535 4.583 20715 Z= 0.289 Chirality : 0.043 0.171 2142 Planarity : 0.005 0.053 2796 Dihedral : 4.978 23.033 2109 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.42 % Favored : 93.42 % 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 (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: -2.17 (0.19), residues: 1869 helix: 0.80 (0.38), residues: 183 sheet: -2.23 (0.21), residues: 540 loop : -1.40 (0.17), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 167 HIS 0.007 0.001 HIS C 170 PHE 0.017 0.002 PHE B 301 TYR 0.014 0.002 TYR A 306 ARG 0.011 0.001 ARG B 486 Details of bonding type rmsd hydrogen bonds : bond 0.04044 ( 156) hydrogen bonds : angle 4.70830 ( 363) covalent geometry : bond 0.00312 (15285) covalent geometry : angle 0.53511 (20715) *********************** 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 47 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 2.448 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: A 23 MET cc_start: 0.8625 (tmm) cc_final: 0.8306 (tmm) REVERT: B 392 PHE cc_start: 0.8805 (m-80) cc_final: 0.8596 (m-80) REVERT: C 487 MET cc_start: 0.8417 (mtt) cc_final: 0.8212 (mtp) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.6086 time to fit residues: 45.7751 Evaluate side-chains 40 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 2.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 74 optimal weight: 9.9990 chunk 166 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 122 optimal weight: 9.9990 chunk 179 optimal weight: 4.9990 chunk 124 optimal weight: 20.0000 chunk 182 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 chunk 68 optimal weight: 10.0000 chunk 153 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN B 124 ASN B 270 GLN B 391 HIS ** B 506 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 GLN ** 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 = 0.3560 r_free = 0.3560 target = 0.031423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.027200 restraints weight = 597592.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.028024 restraints weight = 382771.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.028605 restraints weight = 263955.235| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.062 15285 Z= 0.314 Angle : 0.700 6.651 20715 Z= 0.384 Chirality : 0.044 0.178 2142 Planarity : 0.006 0.069 2796 Dihedral : 5.436 25.602 2109 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 10.65 % Favored : 89.19 % Rotamer: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: -2.88 (0.18), residues: 1869 helix: -0.10 (0.36), residues: 183 sheet: -2.63 (0.20), residues: 558 loop : -1.85 (0.17), residues: 1128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 407 HIS 0.011 0.002 HIS C 170 PHE 0.033 0.003 PHE C 301 TYR 0.026 0.003 TYR C 271 ARG 0.010 0.001 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 156) hydrogen bonds : angle 5.38415 ( 363) covalent geometry : bond 0.00636 (15285) covalent geometry : angle 0.69998 (20715) *********************** 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 : 2.373 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: A 23 MET cc_start: 0.8944 (tmm) cc_final: 0.8529 (tmm) REVERT: B 159 MET cc_start: 0.8853 (mtp) cc_final: 0.8462 (mmm) REVERT: C 344 LEU cc_start: 0.8972 (mt) cc_final: 0.8584 (mt) REVERT: C 487 MET cc_start: 0.8569 (mtt) cc_final: 0.8337 (mtp) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.6026 time to fit residues: 39.9307 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 : 2.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 90 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 144 optimal weight: 8.9990 chunk 104 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 129 optimal weight: 9.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN B 506 ASN ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.032203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.027896 restraints weight = 571936.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.028760 restraints weight = 366813.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.029374 restraints weight = 253843.380| |-----------------------------------------------------------------------------| r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 15285 Z= 0.123 Angle : 0.533 5.037 20715 Z= 0.287 Chirality : 0.044 0.160 2142 Planarity : 0.005 0.052 2796 Dihedral : 5.014 22.205 2109 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.37 % Favored : 93.53 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: -2.45 (0.19), residues: 1869 helix: 0.61 (0.38), residues: 183 sheet: -2.54 (0.21), residues: 567 loop : -1.48 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 213 HIS 0.006 0.001 HIS C 175 PHE 0.049 0.002 PHE B 122 TYR 0.015 0.001 TYR A 306 ARG 0.003 0.001 ARG C 187 Details of bonding type rmsd hydrogen bonds : bond 0.03990 ( 156) hydrogen bonds : angle 4.62453 ( 363) covalent geometry : bond 0.00256 (15285) covalent geometry : angle 0.53330 (20715) *********************** 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 43 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 2.497 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: A 23 MET cc_start: 0.8724 (tmm) cc_final: 0.8385 (tmm) REVERT: B 159 MET cc_start: 0.8724 (mtp) cc_final: 0.8258 (mmm) REVERT: C 344 LEU cc_start: 0.8710 (mt) cc_final: 0.8344 (mt) REVERT: C 487 MET cc_start: 0.8409 (mtt) cc_final: 0.8191 (mtp) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.6005 time to fit residues: 41.2113 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 : 2.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 46 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 172 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 167 optimal weight: 4.9990 chunk 165 optimal weight: 2.9990 chunk 140 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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** B 90 GLN ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.031754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.027658 restraints weight = 585273.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.028453 restraints weight = 380384.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.029016 restraints weight = 266276.277| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15285 Z= 0.189 Angle : 0.554 5.008 20715 Z= 0.300 Chirality : 0.042 0.159 2142 Planarity : 0.005 0.051 2796 Dihedral : 4.967 22.895 2109 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.35 % Favored : 91.55 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: -2.51 (0.19), residues: 1869 helix: 0.62 (0.38), residues: 183 sheet: -2.59 (0.20), residues: 567 loop : -1.54 (0.18), residues: 1119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 213 HIS 0.008 0.001 HIS C 170 PHE 0.033 0.002 PHE C 86 TYR 0.016 0.002 TYR C 271 ARG 0.006 0.001 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.03965 ( 156) hydrogen bonds : angle 4.75415 ( 363) covalent geometry : bond 0.00386 (15285) covalent geometry : angle 0.55419 (20715) *********************** 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 40 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 2.410 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: A 23 MET cc_start: 0.8847 (tmm) cc_final: 0.8475 (tmm) REVERT: B 159 MET cc_start: 0.8807 (mtp) cc_final: 0.8347 (mmm) REVERT: C 344 LEU cc_start: 0.8918 (mt) cc_final: 0.8563 (mt) REVERT: C 487 MET cc_start: 0.8576 (mtt) cc_final: 0.8350 (mtp) outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 0.6368 time to fit residues: 40.5694 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 : 2.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 25 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 164 optimal weight: 0.4980 chunk 103 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 174 optimal weight: 7.9990 chunk 180 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 182 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 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 = 0.3569 r_free = 0.3569 target = 0.031673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.027470 restraints weight = 583915.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.028293 restraints weight = 376260.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.028872 restraints weight = 260516.819| |-----------------------------------------------------------------------------| r_work (final): 0.3455 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.4556 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= 0.177 Angle : 0.546 5.049 20715 Z= 0.295 Chirality : 0.043 0.161 2142 Planarity : 0.005 0.052 2796 Dihedral : 4.962 22.613 2109 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 8.56 % Favored : 91.33 % Rotamer: Outliers : 0.00 % Allowed : 0.06 % Favored : 99.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: -2.51 (0.19), residues: 1869 helix: 0.58 (0.37), residues: 183 sheet: -2.60 (0.21), residues: 549 loop : -1.55 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 141 HIS 0.008 0.001 HIS C 170 PHE 0.029 0.002 PHE B 122 TYR 0.014 0.002 TYR C 271 ARG 0.005 0.001 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 156) hydrogen bonds : angle 4.70385 ( 363) covalent geometry : bond 0.00362 (15285) covalent geometry : angle 0.54612 (20715) ********************** 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 37 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 2.244 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: A 23 MET cc_start: 0.8771 (tmm) cc_final: 0.8406 (tmm) REVERT: B 159 MET cc_start: 0.8665 (mtp) cc_final: 0.8210 (mmm) REVERT: C 344 LEU cc_start: 0.8827 (mt) cc_final: 0.8503 (mt) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.6200 time to fit residues: 36.6703 Evaluate side-chains 32 residues out of total 1578 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 2.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 186 random chunks: chunk 115 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 133 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 168 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 96 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 274 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 504 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 = 0.3559 r_free = 0.3559 target = 0.031446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.027391 restraints weight = 592118.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.028168 restraints weight = 386145.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.028702 restraints weight = 270881.734| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15285 Z= 0.197 Angle : 0.572 7.959 20715 Z= 0.307 Chirality : 0.044 0.364 2142 Planarity : 0.005 0.052 2796 Dihedral : 5.012 22.556 2109 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.11 % Allowed : 9.52 % Favored : 90.37 % Rotamer: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.86 % Cis-general : 0.17 % 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: -2.62 (0.19), residues: 1869 helix: 0.51 (0.37), residues: 183 sheet: -2.70 (0.21), residues: 552 loop : -1.61 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 213 HIS 0.009 0.001 HIS C 170 PHE 0.028 0.002 PHE B 301 TYR 0.015 0.002 TYR C 271 ARG 0.006 0.001 ARG A 486 Details of bonding type rmsd hydrogen bonds : bond 0.03985 ( 156) hydrogen bonds : angle 4.76034 ( 363) covalent geometry : bond 0.00404 (15285) covalent geometry : angle 0.57168 (20715) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6842.22 seconds wall clock time: 118 minutes 50.86 seconds (7130.86 seconds total)