Starting phenix.real_space_refine on Tue Feb 3 15:51:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmq_48399/02_2026/9mmq_48399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmq_48399/02_2026/9mmq_48399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9mmq_48399/02_2026/9mmq_48399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmq_48399/02_2026/9mmq_48399.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mmq_48399/02_2026/9mmq_48399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmq_48399/02_2026/9mmq_48399.map" } resolution = 2.9 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: 8 Type Number sf(0) Gaussians I 1 10.91 5 P 6 5.49 5 Mg 2 5.21 5 S 31 5.16 5 C 2838 2.51 5 N 761 2.21 5 O 821 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4461 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2194 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 10, 'TRANS': 261} Chain: "B" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2178 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 16, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'AGS': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 57 Unusual residues: {' MG': 1, 'AGS': 1, 'LCJ': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 0.78, per 1000 atoms: 0.17 Number of scatterers: 4461 At special positions: 0 Unit cell: (67.16, 73.73, 88.33, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) I 1 52.95 S 31 16.00 P 6 15.00 Mg 2 11.99 F 1 9.00 O 821 8.00 N 761 7.00 C 2838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.61 Conformation dependent library (CDL) restraints added in 445.3 milliseconds 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1022 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 5 sheets defined 47.2% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'A' and resid 383 through 400 removed outlier: 3.604A pdb=" N THR A 400 " --> pdb=" O VAL A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 434 Processing helix chain 'A' and resid 441 through 462 Processing helix chain 'A' and resid 489 through 494 Processing helix chain 'A' and resid 513 through 519 Processing helix chain 'A' and resid 526 through 544 Processing helix chain 'A' and resid 553 through 563 Processing helix chain 'A' and resid 569 through 573 removed outlier: 3.670A pdb=" N LYS A 572 " --> pdb=" O ASP A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 Processing helix chain 'A' and resid 598 through 611 Processing helix chain 'B' and resid 64 through 66 No H-bonds generated for 'chain 'B' and resid 64 through 66' Processing helix chain 'B' and resid 104 through 116 Processing helix chain 'B' and resid 117 through 121 Processing helix chain 'B' and resid 151 through 158 Processing helix chain 'B' and resid 162 through 185 Processing helix chain 'B' and resid 212 through 221 removed outlier: 4.035A pdb=" N ASN B 221 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 236 Processing helix chain 'B' and resid 241 through 258 removed outlier: 3.891A pdb=" N ASP B 245 " --> pdb=" O SER B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 320 Processing helix chain 'B' and resid 331 through 342 Processing helix chain 'B' and resid 351 through 357 Processing helix chain 'B' and resid 358 through 367 Processing helix chain 'B' and resid 370 through 380 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357 removed outlier: 6.397A pdb=" N ARG A 354 " --> pdb=" O LYS A 365 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N LYS A 365 " --> pdb=" O ARG A 354 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 356 " --> pdb=" O VAL A 363 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 474 through 477 Processing sheet with id=AA3, first strand: chain 'A' and resid 496 through 497 removed outlier: 3.513A pdb=" N GLN A 500 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 68 through 76 removed outlier: 7.244A pdb=" N ILE B 71 " --> pdb=" O SER B 86 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N SER B 86 " --> pdb=" O ILE B 71 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLU B 73 " --> pdb=" O LYS B 84 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LYS B 84 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N GLU B 144 " --> pdb=" O PHE B 129 " (cutoff:3.500A) removed outlier: 6.938A pdb=" N PHE B 129 " --> pdb=" O GLU B 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 149 through 150 removed outlier: 3.703A pdb=" N GLY B 149 " --> pdb=" O VAL B 198 " (cutoff:3.500A) 208 hydrogen bonds defined for protein. 603 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.66 Time building geometry restraints manager: 0.75 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.39: 1791 1.39 - 1.55: 2704 1.55 - 1.71: 14 1.71 - 1.87: 50 1.87 - 2.04: 3 Bond restraints: 4562 Sorted by residual: bond pdb=" N GLN A 504 " pdb=" CA GLN A 504 " ideal model delta sigma weight residual 1.452 1.487 -0.035 1.11e-02 8.12e+03 9.79e+00 bond pdb=" C23 LCJ B 703 " pdb=" I01 LCJ B 703 " ideal model delta sigma weight residual 2.099 2.037 0.062 2.00e-02 2.50e+03 9.65e+00 bond pdb=" N PHE B 209 " pdb=" CA PHE B 209 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.15e-02 7.56e+03 8.60e+00 bond pdb=" N ILE B 263 " pdb=" CA ILE B 263 " ideal model delta sigma weight residual 1.463 1.497 -0.034 1.20e-02 6.94e+03 8.23e+00 bond pdb=" C10 LCJ B 703 " pdb=" N07 LCJ B 703 " ideal model delta sigma weight residual 1.371 1.428 -0.057 2.00e-02 2.50e+03 8.22e+00 ... (remaining 4557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 5966 1.86 - 3.73: 181 3.73 - 5.59: 22 5.59 - 7.46: 1 7.46 - 9.32: 2 Bond angle restraints: 6172 Sorted by residual: angle pdb=" C TYR B 261 " pdb=" CA TYR B 261 " pdb=" CB TYR B 261 " ideal model delta sigma weight residual 109.67 118.99 -9.32 1.65e+00 3.67e-01 3.19e+01 angle pdb=" N VAL B 211 " pdb=" CA VAL B 211 " pdb=" C VAL B 211 " ideal model delta sigma weight residual 111.58 107.80 3.78 1.06e+00 8.90e-01 1.27e+01 angle pdb=" N TYR B 261 " pdb=" CA TYR B 261 " pdb=" CB TYR B 261 " ideal model delta sigma weight residual 109.68 103.83 5.85 1.83e+00 2.99e-01 1.02e+01 angle pdb=" CA GLN A 501 " pdb=" C GLN A 501 " pdb=" O GLN A 501 " ideal model delta sigma weight residual 121.16 117.60 3.56 1.12e+00 7.97e-01 1.01e+01 angle pdb=" CA ARG A 495 " pdb=" C ARG A 495 " pdb=" O ARG A 495 " ideal model delta sigma weight residual 121.87 118.22 3.65 1.16e+00 7.43e-01 9.92e+00 ... (remaining 6167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.63: 2673 27.63 - 55.27: 74 55.27 - 82.90: 1 82.90 - 110.53: 2 110.53 - 138.16: 2 Dihedral angle restraints: 2752 sinusoidal: 1163 harmonic: 1589 Sorted by residual: dihedral pdb=" O1B AGS A 701 " pdb=" O3B AGS A 701 " pdb=" PB AGS A 701 " pdb=" PG AGS A 701 " ideal model delta sinusoidal sigma weight residual 68.91 -69.25 138.16 1 3.00e+01 1.11e-03 1.86e+01 dihedral pdb=" O1A AGS A 701 " pdb=" O3A AGS A 701 " pdb=" PA AGS A 701 " pdb=" PB AGS A 701 " ideal model delta sinusoidal sigma weight residual 292.27 164.00 128.27 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" CD ARG A 391 " pdb=" NE ARG A 391 " pdb=" CZ ARG A 391 " pdb=" NH1 ARG A 391 " ideal model delta sinusoidal sigma weight residual 0.00 -34.05 34.05 1 1.00e+01 1.00e-02 1.65e+01 ... (remaining 2749 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 525 0.051 - 0.102: 114 0.102 - 0.152: 29 0.152 - 0.203: 3 0.203 - 0.254: 3 Chirality restraints: 674 Sorted by residual: chirality pdb=" CA ILE B 139 " pdb=" N ILE B 139 " pdb=" C ILE B 139 " pdb=" CB ILE B 139 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CA VAL B 211 " pdb=" N VAL B 211 " pdb=" C VAL B 211 " pdb=" CB VAL B 211 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA ARG A 401 " pdb=" N ARG A 401 " pdb=" C ARG A 401 " pdb=" CB ARG A 401 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 671 not shown) Planarity restraints: 775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 391 " -0.628 9.50e-02 1.11e+02 2.81e-01 4.84e+01 pdb=" NE ARG A 391 " 0.036 2.00e-02 2.50e+03 pdb=" CZ ARG A 391 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 391 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 391 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 599 " 0.025 5.00e-02 4.00e+02 3.83e-02 2.35e+00 pdb=" N PRO A 600 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 600 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 600 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 401 " -0.131 9.50e-02 1.11e+02 5.87e-02 2.12e+00 pdb=" NE ARG A 401 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A 401 " 0.003 2.00e-02 2.50e+03 pdb=" NH1 ARG A 401 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 401 " -0.005 2.00e-02 2.50e+03 ... (remaining 772 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.50: 29 2.50 - 3.12: 3400 3.12 - 3.73: 7488 3.73 - 4.35: 11191 4.35 - 4.96: 18479 Nonbonded interactions: 40587 Sorted by model distance: nonbonded pdb=" O2A AGS B 701 " pdb="MG MG B 702 " model vdw 1.887 2.170 nonbonded pdb=" OD2 ASP B 208 " pdb="MG MG B 702 " model vdw 1.935 2.170 nonbonded pdb=" O1B AGS A 701 " pdb="MG MG A 702 " model vdw 1.958 2.170 nonbonded pdb=" OD2 ASP A 486 " pdb="MG MG A 702 " model vdw 2.044 2.170 nonbonded pdb=" OE1 GLN B 153 " pdb=" O2' AGS B 701 " model vdw 2.201 3.040 ... (remaining 40582 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 6.260 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 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 : 0.005 0.062 4562 Z= 0.318 Angle : 0.713 9.321 6172 Z= 0.442 Chirality : 0.049 0.254 674 Planarity : 0.011 0.281 775 Dihedral : 12.894 138.164 1730 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.21 % Allowed : 6.43 % Favored : 93.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.37), residues: 545 helix: 1.45 (0.34), residues: 242 sheet: -0.64 (0.59), residues: 60 loop : -0.10 (0.42), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 391 TYR 0.022 0.002 TYR B 261 PHE 0.011 0.002 PHE A 443 TRP 0.007 0.001 TRP A 368 HIS 0.003 0.001 HIS A 432 Details of bonding type rmsd covalent geometry : bond 0.00541 ( 4562) covalent geometry : angle 0.71334 ( 6172) hydrogen bonds : bond 0.17026 ( 208) hydrogen bonds : angle 6.78385 ( 603) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 118 time to evaluate : 0.243 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.7840 (ptp) cc_final: 0.7592 (ptm) REVERT: A 431 LYS cc_start: 0.8225 (mttt) cc_final: 0.7732 (mtpm) REVERT: A 477 HIS cc_start: 0.7313 (t70) cc_final: 0.7085 (t-90) REVERT: A 495 ARG cc_start: 0.8064 (mtm110) cc_final: 0.7365 (ptt-90) REVERT: A 575 LYS cc_start: 0.8717 (mttt) cc_final: 0.8480 (mtmm) REVERT: A 579 LYS cc_start: 0.8705 (mttt) cc_final: 0.8338 (tptp) REVERT: B 66 ASP cc_start: 0.8198 (p0) cc_final: 0.7812 (p0) REVERT: B 67 ASP cc_start: 0.6919 (m-30) cc_final: 0.6566 (m-30) REVERT: B 78 ASN cc_start: 0.7519 (m110) cc_final: 0.6872 (t0) REVERT: B 102 GLU cc_start: 0.8121 (mt-10) cc_final: 0.7540 (mm-30) REVERT: B 164 GLN cc_start: 0.8282 (mm-40) cc_final: 0.8038 (mp10) REVERT: B 182 GLU cc_start: 0.8442 (mt-10) cc_final: 0.8088 (mm-30) REVERT: B 187 MET cc_start: 0.8002 (mtm) cc_final: 0.6639 (ttt) REVERT: B 189 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7562 (mtt180) outliers start: 1 outliers final: 0 residues processed: 119 average time/residue: 0.6835 time to fit residues: 83.4987 Evaluate side-chains 78 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.0970 chunk 48 optimal weight: 0.5980 chunk 26 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 550 HIS A 553 ASN A 556 GLN B 153 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.119900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.102165 restraints weight = 5753.266| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 1.85 r_work: 0.3157 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4562 Z= 0.149 Angle : 0.575 6.029 6172 Z= 0.297 Chirality : 0.043 0.149 674 Planarity : 0.005 0.038 775 Dihedral : 12.143 142.764 643 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.53 % Allowed : 11.83 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.36), residues: 545 helix: 1.59 (0.34), residues: 242 sheet: -0.70 (0.54), residues: 65 loop : 0.05 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 160 TYR 0.019 0.002 TYR B 261 PHE 0.008 0.002 PHE B 129 TRP 0.004 0.001 TRP A 423 HIS 0.003 0.001 HIS A 460 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4562) covalent geometry : angle 0.57516 ( 6172) hydrogen bonds : bond 0.04349 ( 208) hydrogen bonds : angle 5.24377 ( 603) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 609 LEU cc_start: 0.8496 (mt) cc_final: 0.8254 (mp) REVERT: B 64 LYS cc_start: 0.7218 (mtmm) cc_final: 0.6506 (pttp) REVERT: B 66 ASP cc_start: 0.8211 (p0) cc_final: 0.7980 (p0) REVERT: B 67 ASP cc_start: 0.7518 (m-30) cc_final: 0.7207 (m-30) REVERT: B 78 ASN cc_start: 0.7772 (m110) cc_final: 0.7284 (t0) REVERT: B 187 MET cc_start: 0.8191 (mtm) cc_final: 0.7397 (ttt) outliers start: 17 outliers final: 5 residues processed: 92 average time/residue: 0.4967 time to fit residues: 47.4333 Evaluate side-chains 72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 67 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 TRP Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 338 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 477 HIS B 153 GLN B 335 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.118151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.099895 restraints weight = 5505.805| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 1.87 r_work: 0.3120 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4562 Z= 0.185 Angle : 0.588 7.142 6172 Z= 0.301 Chirality : 0.043 0.155 674 Planarity : 0.005 0.047 775 Dihedral : 12.294 144.423 643 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.94 % Allowed : 13.49 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.36), residues: 545 helix: 1.57 (0.34), residues: 244 sheet: -0.82 (0.53), residues: 71 loop : -0.02 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 160 TYR 0.013 0.002 TYR B 261 PHE 0.010 0.002 PHE A 387 TRP 0.005 0.001 TRP A 368 HIS 0.011 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 4562) covalent geometry : angle 0.58827 ( 6172) hydrogen bonds : bond 0.04407 ( 208) hydrogen bonds : angle 5.05710 ( 603) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 609 LEU cc_start: 0.8472 (mt) cc_final: 0.8202 (mp) REVERT: B 64 LYS cc_start: 0.7213 (mtmm) cc_final: 0.6461 (pttp) REVERT: B 67 ASP cc_start: 0.7447 (m-30) cc_final: 0.7165 (m-30) REVERT: B 78 ASN cc_start: 0.7777 (m110) cc_final: 0.7381 (t0) REVERT: B 187 MET cc_start: 0.8239 (mtm) cc_final: 0.7576 (ttp) outliers start: 19 outliers final: 9 residues processed: 86 average time/residue: 0.4846 time to fit residues: 43.3454 Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 75 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 338 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 8 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 472 ASN A 556 GLN B 153 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.118267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.100941 restraints weight = 5137.633| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 1.72 r_work: 0.3132 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2989 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.2989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4562 Z= 0.176 Angle : 0.572 5.764 6172 Z= 0.293 Chirality : 0.043 0.154 674 Planarity : 0.004 0.045 775 Dihedral : 12.367 145.221 643 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.98 % Allowed : 13.90 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.36), residues: 545 helix: 1.60 (0.34), residues: 243 sheet: -0.95 (0.52), residues: 71 loop : -0.02 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 160 TYR 0.011 0.002 TYR B 261 PHE 0.010 0.001 PHE B 337 TRP 0.005 0.001 TRP B 374 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00414 ( 4562) covalent geometry : angle 0.57172 ( 6172) hydrogen bonds : bond 0.04189 ( 208) hydrogen bonds : angle 5.01658 ( 603) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8143 (ptp) cc_final: 0.7844 (ptt) REVERT: A 609 LEU cc_start: 0.8471 (mt) cc_final: 0.8223 (mp) REVERT: B 67 ASP cc_start: 0.7473 (m-30) cc_final: 0.7206 (m-30) REVERT: B 78 ASN cc_start: 0.7810 (m110) cc_final: 0.7464 (t0) REVERT: B 187 MET cc_start: 0.8220 (mtm) cc_final: 0.7566 (ttt) outliers start: 24 outliers final: 11 residues processed: 94 average time/residue: 0.4086 time to fit residues: 39.8723 Evaluate side-chains 80 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 69 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 338 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 1.9990 overall best weight: 0.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 ASN B 153 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.100307 restraints weight = 5344.089| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.82 r_work: 0.3120 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4562 Z= 0.162 Angle : 0.578 6.395 6172 Z= 0.296 Chirality : 0.043 0.151 674 Planarity : 0.004 0.044 775 Dihedral : 12.421 145.367 643 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.36 % Allowed : 14.94 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.36), residues: 545 helix: 1.66 (0.34), residues: 243 sheet: -0.97 (0.52), residues: 71 loop : 0.01 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 495 TYR 0.015 0.002 TYR B 229 PHE 0.010 0.001 PHE A 599 TRP 0.006 0.001 TRP A 342 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4562) covalent geometry : angle 0.57844 ( 6172) hydrogen bonds : bond 0.04033 ( 208) hydrogen bonds : angle 4.93381 ( 603) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8136 (ptp) cc_final: 0.7820 (ptt) REVERT: A 609 LEU cc_start: 0.8426 (mt) cc_final: 0.8174 (mp) REVERT: B 64 LYS cc_start: 0.7289 (OUTLIER) cc_final: 0.6855 (pttp) REVERT: B 67 ASP cc_start: 0.7496 (m-30) cc_final: 0.7280 (m-30) REVERT: B 78 ASN cc_start: 0.7782 (m110) cc_final: 0.7430 (t0) REVERT: B 187 MET cc_start: 0.8274 (mtm) cc_final: 0.7560 (ttt) outliers start: 21 outliers final: 10 residues processed: 88 average time/residue: 0.4060 time to fit residues: 37.2782 Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 64 LYS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 338 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 1 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.116700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.098199 restraints weight = 5733.017| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.90 r_work: 0.3085 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.3043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4562 Z= 0.185 Angle : 0.595 6.592 6172 Z= 0.305 Chirality : 0.043 0.152 674 Planarity : 0.004 0.049 775 Dihedral : 12.474 144.815 643 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.94 % Allowed : 16.39 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.36), residues: 545 helix: 1.58 (0.34), residues: 244 sheet: -0.91 (0.53), residues: 71 loop : -0.00 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 160 TYR 0.008 0.002 TYR B 240 PHE 0.010 0.001 PHE A 599 TRP 0.008 0.002 TRP A 342 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00437 ( 4562) covalent geometry : angle 0.59457 ( 6172) hydrogen bonds : bond 0.04141 ( 208) hydrogen bonds : angle 5.02592 ( 603) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8151 (ptp) cc_final: 0.7833 (ptt) REVERT: A 609 LEU cc_start: 0.8472 (mt) cc_final: 0.8206 (mp) REVERT: B 64 LYS cc_start: 0.7286 (ptpp) cc_final: 0.6992 (ptpp) REVERT: B 67 ASP cc_start: 0.7502 (m-30) cc_final: 0.7289 (m-30) REVERT: B 78 ASN cc_start: 0.7760 (m110) cc_final: 0.7437 (t0) REVERT: B 187 MET cc_start: 0.8344 (mtm) cc_final: 0.7642 (ttp) outliers start: 19 outliers final: 12 residues processed: 90 average time/residue: 0.5611 time to fit residues: 52.4811 Evaluate side-chains 84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 147 ASP Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 224 VAL Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 338 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.118750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.100469 restraints weight = 5521.134| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 1.89 r_work: 0.3112 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4562 Z= 0.155 Angle : 0.584 6.871 6172 Z= 0.299 Chirality : 0.043 0.149 674 Planarity : 0.004 0.048 775 Dihedral : 12.457 145.637 643 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.53 % Allowed : 16.39 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.36), residues: 545 helix: 1.56 (0.34), residues: 244 sheet: -0.94 (0.53), residues: 71 loop : -0.01 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 495 TYR 0.010 0.002 TYR B 261 PHE 0.010 0.001 PHE A 599 TRP 0.012 0.001 TRP A 342 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4562) covalent geometry : angle 0.58367 ( 6172) hydrogen bonds : bond 0.03952 ( 208) hydrogen bonds : angle 4.97370 ( 603) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8117 (ptp) cc_final: 0.7784 (ptt) REVERT: A 575 LYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7927 (mtmm) REVERT: A 609 LEU cc_start: 0.8443 (mt) cc_final: 0.8180 (mp) REVERT: B 67 ASP cc_start: 0.7501 (m-30) cc_final: 0.7265 (m-30) REVERT: B 78 ASN cc_start: 0.7736 (m110) cc_final: 0.7413 (t0) REVERT: B 187 MET cc_start: 0.8324 (mtm) cc_final: 0.7573 (ttt) outliers start: 17 outliers final: 10 residues processed: 86 average time/residue: 0.4576 time to fit residues: 41.0262 Evaluate side-chains 83 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 492 VAL Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 338 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.0770 chunk 2 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 42 optimal weight: 0.0970 chunk 24 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.119623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.102012 restraints weight = 5230.738| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.80 r_work: 0.3155 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3019 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4562 Z= 0.124 Angle : 0.564 7.217 6172 Z= 0.289 Chirality : 0.042 0.142 674 Planarity : 0.004 0.049 775 Dihedral : 12.326 146.871 643 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.32 % Allowed : 17.01 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.36), residues: 545 helix: 1.60 (0.34), residues: 244 sheet: -1.19 (0.55), residues: 66 loop : 0.03 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 189 TYR 0.012 0.001 TYR B 261 PHE 0.009 0.001 PHE A 599 TRP 0.014 0.001 TRP A 342 HIS 0.002 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4562) covalent geometry : angle 0.56390 ( 6172) hydrogen bonds : bond 0.03666 ( 208) hydrogen bonds : angle 4.88731 ( 603) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8082 (ptp) cc_final: 0.7753 (ptt) REVERT: A 575 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7910 (mtmm) REVERT: A 609 LEU cc_start: 0.8464 (mt) cc_final: 0.8201 (mp) REVERT: B 67 ASP cc_start: 0.7499 (m-30) cc_final: 0.7219 (m-30) REVERT: B 78 ASN cc_start: 0.7727 (m110) cc_final: 0.7409 (t0) REVERT: B 187 MET cc_start: 0.8296 (mtm) cc_final: 0.7539 (ttt) outliers start: 16 outliers final: 9 residues processed: 82 average time/residue: 0.4222 time to fit residues: 36.1713 Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 447 ASP Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 338 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.0000 chunk 13 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 6 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 overall best weight: 0.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.120111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102335 restraints weight = 5242.149| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.81 r_work: 0.3162 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3029 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4562 Z= 0.130 Angle : 0.566 7.448 6172 Z= 0.290 Chirality : 0.042 0.145 674 Planarity : 0.004 0.049 775 Dihedral : 12.293 146.382 643 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.70 % Allowed : 17.43 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.36), residues: 545 helix: 1.59 (0.34), residues: 243 sheet: -0.95 (0.53), residues: 71 loop : 0.07 (0.41), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 495 TYR 0.012 0.001 TYR B 261 PHE 0.009 0.001 PHE A 599 TRP 0.018 0.001 TRP A 342 HIS 0.002 0.001 HIS A 466 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 4562) covalent geometry : angle 0.56605 ( 6172) hydrogen bonds : bond 0.03697 ( 208) hydrogen bonds : angle 4.84747 ( 603) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8086 (ptp) cc_final: 0.7752 (ptt) REVERT: A 575 LYS cc_start: 0.8440 (OUTLIER) cc_final: 0.7907 (mtmm) REVERT: A 609 LEU cc_start: 0.8490 (mt) cc_final: 0.8221 (mp) REVERT: B 67 ASP cc_start: 0.7390 (m-30) cc_final: 0.7156 (m-30) REVERT: B 78 ASN cc_start: 0.7701 (m110) cc_final: 0.7394 (t0) REVERT: B 187 MET cc_start: 0.8296 (mtm) cc_final: 0.7560 (ttp) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.5430 time to fit residues: 45.7215 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 317 ILE Chi-restraints excluded: chain B residue 338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 3 optimal weight: 0.6980 chunk 27 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 49 optimal weight: 0.0770 chunk 8 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.0020 chunk 0 optimal weight: 2.9990 overall best weight: 0.3546 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.120873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103558 restraints weight = 5347.941| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.74 r_work: 0.3184 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4562 Z= 0.121 Angle : 0.549 6.965 6172 Z= 0.282 Chirality : 0.042 0.143 674 Planarity : 0.004 0.049 775 Dihedral : 12.255 146.845 643 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 2.28 % Allowed : 18.26 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.36), residues: 545 helix: 1.59 (0.34), residues: 244 sheet: -1.15 (0.56), residues: 65 loop : 0.11 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 495 TYR 0.012 0.001 TYR B 261 PHE 0.008 0.001 PHE A 599 TRP 0.017 0.001 TRP A 342 HIS 0.003 0.001 HIS B 239 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4562) covalent geometry : angle 0.54875 ( 6172) hydrogen bonds : bond 0.03635 ( 208) hydrogen bonds : angle 4.80812 ( 603) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1090 Ramachandran restraints generated. 545 Oldfield, 0 Emsley, 545 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.148 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8077 (ptp) cc_final: 0.7757 (ptt) REVERT: A 575 LYS cc_start: 0.8430 (OUTLIER) cc_final: 0.7875 (mtmm) REVERT: A 609 LEU cc_start: 0.8517 (mt) cc_final: 0.8228 (mp) REVERT: B 67 ASP cc_start: 0.7450 (m-30) cc_final: 0.7232 (m-30) REVERT: B 78 ASN cc_start: 0.7736 (m110) cc_final: 0.7468 (t0) REVERT: B 187 MET cc_start: 0.8323 (mtm) cc_final: 0.7657 (ttt) REVERT: B 230 MET cc_start: 0.8585 (mmm) cc_final: 0.8112 (mmt) outliers start: 11 outliers final: 9 residues processed: 86 average time/residue: 0.4429 time to fit residues: 39.7290 Evaluate side-chains 83 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 VAL Chi-restraints excluded: chain A residue 401 ARG Chi-restraints excluded: chain A residue 575 LYS Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain B residue 100 HIS Chi-restraints excluded: chain B residue 127 VAL Chi-restraints excluded: chain B residue 144 GLU Chi-restraints excluded: chain B residue 183 LYS Chi-restraints excluded: chain B residue 214 GLN Chi-restraints excluded: chain B residue 338 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.118183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.099994 restraints weight = 5622.235| |-----------------------------------------------------------------------------| r_work (start): 0.3234 rms_B_bonded: 1.89 r_work: 0.3117 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4562 Z= 0.187 Angle : 0.610 8.012 6172 Z= 0.313 Chirality : 0.044 0.152 674 Planarity : 0.004 0.048 775 Dihedral : 12.443 144.317 643 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.07 % Allowed : 18.67 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.36), residues: 545 helix: 1.55 (0.34), residues: 243 sheet: -1.11 (0.56), residues: 65 loop : 0.04 (0.40), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 495 TYR 0.014 0.002 TYR B 240 PHE 0.013 0.002 PHE B 311 TRP 0.018 0.002 TRP A 342 HIS 0.003 0.001 HIS A 477 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 4562) covalent geometry : angle 0.60967 ( 6172) hydrogen bonds : bond 0.04076 ( 208) hydrogen bonds : angle 4.97344 ( 603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1625.29 seconds wall clock time: 28 minutes 33.44 seconds (1713.44 seconds total)