Starting phenix.real_space_refine on Thu Jul 2 00:23:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mmq_48399/07_2026/9mmq_48399.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mmq_48399/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9mmq_48399/07_2026/9mmq_48399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mmq_48399/07_2026/9mmq_48399.map" model { file = "/net/cci-nas-00/data/ceres_data/9mmq_48399/07_2026/9mmq_48399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mmq_48399/07_2026/9mmq_48399.cif" } 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-dev-6108/lib/python3.11/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: 1.18, per 1000 atoms: 0.26 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: 0.38 Conformation dependent library (CDL) restraints added in 155.9 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: 0.14 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: 0.65 Time building geometry restraints manager: 0.52 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=" O3B AGS A 701 " pdb=" PB AGS A 701 " ideal model delta sigma weight residual 1.673 1.580 0.093 2.00e-02 2.50e+03 2.16e+01 bond pdb=" O3B AGS B 701 " pdb=" PB AGS B 701 " ideal model delta sigma weight residual 1.673 1.584 0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" O3A AGS A 701 " pdb=" PA AGS A 701 " ideal model delta sigma weight residual 1.664 1.581 0.083 2.00e-02 2.50e+03 1.74e+01 bond pdb=" O3A AGS B 701 " pdb=" PA AGS B 701 " ideal model delta sigma weight residual 1.664 1.583 0.081 2.00e-02 2.50e+03 1.63e+01 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 ... (remaining 4557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 5923 1.88 - 3.75: 199 3.75 - 5.63: 33 5.63 - 7.51: 6 7.51 - 9.39: 11 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 - 32.17: 2706 32.17 - 64.35: 64 64.35 - 96.52: 12 96.52 - 128.70: 2 128.70 - 160.87: 4 Dihedral angle restraints: 2788 sinusoidal: 1199 harmonic: 1589 Sorted by residual: dihedral pdb=" O3A 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 -107.39 53.48 -160.87 1 3.00e+01 1.11e-03 2.07e+01 dihedral pdb=" O2B 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 7.37 167.47 -160.10 1 3.00e+01 1.11e-03 2.07e+01 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 138.55 -69.25 -152.20 1 3.00e+01 1.11e-03 2.01e+01 ... (remaining 2785 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 536 0.055 - 0.109: 101 0.109 - 0.163: 26 0.163 - 0.218: 2 0.218 - 0.272: 5 Chirality restraints: 670 Sorted by residual: chirality pdb=" C3' AGS A 701 " pdb=" C2' AGS A 701 " pdb=" C4' AGS A 701 " pdb=" O3' AGS A 701 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' AGS B 701 " pdb=" C2' AGS B 701 " pdb=" C4' AGS B 701 " pdb=" O3' AGS B 701 " both_signs ideal model delta sigma weight residual False -2.37 -2.64 0.27 2.00e-01 2.50e+01 1.80e+00 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 ... (remaining 667 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: 3.750 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: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.020 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:6.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 4562 Z= 0.366 Angle : 0.846 9.387 6172 Z= 0.466 Chirality : 0.051 0.272 670 Planarity : 0.011 0.281 775 Dihedral : 16.165 160.870 1766 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/Z covalent geometry : bond 0.00652 / 0.37 ( 4562) covalent geometry : angle 0.84607 / 0.47 ( 6172) hydrogen bonds : bond 0.17026 / 11.35 ( 208) hydrogen bonds : angle 6.78385 / 4.84 ( 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 : 0.201 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: 0.7261 time to fit residues: 88.8355 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 : 0.172 ------------------------------------------------------------------------------- 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: 0.8980 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... ** A 473 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 GLN A 550 HIS A 553 ASN A 556 GLN B 153 GLN B 335 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.119817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.102287 restraints weight = 5849.567| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.87 r_work: 0.3162 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4562 Z= 0.148 Angle : 0.586 6.540 6172 Z= 0.296 Chirality : 0.043 0.150 670 Planarity : 0.005 0.040 775 Dihedral : 17.253 172.015 679 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.73 % Allowed : 11.83 % Favored : 84.44 % 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: 0.91 (0.36), residues: 545 helix: 1.60 (0.34), residues: 242 sheet: -0.73 (0.54), residues: 65 loop : 0.07 (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 0.001 PHE A 599 TRP 0.004 0.001 TRP A 368 HIS 0.003 0.001 HIS A 550 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 ( 4562) covalent geometry : angle 0.58607 / 0.30 ( 6172) hydrogen bonds : bond 0.04382 / 2.90 ( 208) hydrogen bonds : angle 5.18715 / 3.73 ( 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: 18 poor density : 81 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 431 LYS cc_start: 0.8787 (mttt) cc_final: 0.8577 (mtpm) REVERT: A 609 LEU cc_start: 0.8482 (mt) cc_final: 0.8255 (mp) REVERT: B 64 LYS cc_start: 0.7221 (mtmm) cc_final: 0.6497 (pttm) REVERT: B 66 ASP cc_start: 0.8206 (p0) cc_final: 0.7986 (p0) REVERT: B 67 ASP cc_start: 0.7507 (m-30) cc_final: 0.7204 (m-30) REVERT: B 78 ASN cc_start: 0.7659 (m110) cc_final: 0.7190 (t0) REVERT: B 187 MET cc_start: 0.8205 (mtm) cc_final: 0.7403 (ttt) outliers start: 18 outliers final: 5 residues processed: 91 average time/residue: 0.5423 time to fit residues: 51.2145 Evaluate side-chains 75 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 70 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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: 0.8980 chunk 51 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 392 ASN A 472 ASN A 477 HIS A 553 ASN A 556 GLN B 153 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.118851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.100938 restraints weight = 5442.190| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 1.83 r_work: 0.3140 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4562 Z= 0.165 Angle : 0.585 6.421 6172 Z= 0.293 Chirality : 0.043 0.155 670 Planarity : 0.004 0.044 775 Dihedral : 15.051 164.708 679 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.15 % Allowed : 12.66 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.87 (0.36), residues: 545 helix: 1.62 (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 0.003 0.001 ARG B 160 TYR 0.012 0.002 TYR B 261 PHE 0.010 0.002 PHE A 387 TRP 0.004 0.001 TRP B 374 HIS 0.010 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.17 ( 4562) covalent geometry : angle 0.58458 / 0.29 ( 6172) hydrogen bonds : bond 0.04316 / 2.89 ( 208) hydrogen bonds : angle 4.99850 / 3.60 ( 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 97 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 609 LEU cc_start: 0.8492 (mt) cc_final: 0.8218 (mp) REVERT: B 64 LYS cc_start: 0.7243 (mtmm) cc_final: 0.6508 (pttp) REVERT: B 66 ASP cc_start: 0.8193 (p0) cc_final: 0.7954 (p0) REVERT: B 67 ASP cc_start: 0.7406 (m-30) cc_final: 0.7116 (m-30) REVERT: B 78 ASN cc_start: 0.7622 (m110) cc_final: 0.7244 (t0) REVERT: B 187 MET cc_start: 0.8219 (mtm) cc_final: 0.7553 (ttp) outliers start: 20 outliers final: 9 residues processed: 88 average time/residue: 0.5048 time to fit residues: 46.2873 Evaluate side-chains 82 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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: 4.9990 chunk 25 optimal weight: 0.8980 chunk 17 optimal weight: 0.0870 chunk 5 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101860 restraints weight = 5188.923| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.78 r_work: 0.3148 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4562 Z= 0.154 Angle : 0.561 5.428 6172 Z= 0.285 Chirality : 0.042 0.151 670 Planarity : 0.004 0.044 775 Dihedral : 13.223 152.355 679 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.15 % Allowed : 14.32 % Favored : 81.54 % 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: 0.87 (0.36), residues: 545 helix: 1.65 (0.34), residues: 244 sheet: -0.97 (0.52), residues: 71 loop : 0.05 (0.42), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 160 TYR 0.011 0.001 TYR B 261 PHE 0.009 0.001 PHE A 599 TRP 0.005 0.001 TRP A 342 HIS 0.002 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 ( 4562) covalent geometry : angle 0.56098 / 0.28 ( 6172) hydrogen bonds : bond 0.04040 / 2.69 ( 208) hydrogen bonds : angle 4.93406 / 3.56 ( 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 98 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8125 (ptp) cc_final: 0.7817 (ptt) REVERT: A 609 LEU cc_start: 0.8462 (mt) cc_final: 0.8213 (mp) REVERT: B 67 ASP cc_start: 0.7441 (m-30) cc_final: 0.7065 (m-30) REVERT: B 78 ASN cc_start: 0.7622 (m110) cc_final: 0.7243 (t0) REVERT: B 94 MET cc_start: 0.8192 (ptp) cc_final: 0.7943 (mtt) REVERT: B 187 MET cc_start: 0.8207 (mtm) cc_final: 0.7508 (ttp) outliers start: 20 outliers final: 10 residues processed: 91 average time/residue: 0.5581 time to fit residues: 52.7872 Evaluate side-chains 78 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 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 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: 1.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 33 optimal weight: 0.0370 overall best weight: 0.6260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.119073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101377 restraints weight = 5288.993| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.81 r_work: 0.3140 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4562 Z= 0.155 Angle : 0.568 6.020 6172 Z= 0.290 Chirality : 0.043 0.149 670 Planarity : 0.004 0.046 775 Dihedral : 12.952 152.416 679 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.73 % Allowed : 15.35 % Favored : 80.91 % 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: 1.70 (0.34), residues: 244 sheet: -0.99 (0.52), residues: 71 loop : 0.05 (0.42), residues: 230 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 0.013 0.001 PHE B 311 TRP 0.007 0.001 TRP A 342 HIS 0.002 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 4562) covalent geometry : angle 0.56826 / 0.29 ( 6172) hydrogen bonds : bond 0.03966 / 2.65 ( 208) hydrogen bonds : angle 4.88335 / 3.53 ( 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 91 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 73 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8082 (ptp) cc_final: 0.7778 (ptt) REVERT: A 609 LEU cc_start: 0.8431 (mt) cc_final: 0.8180 (mp) REVERT: B 67 ASP cc_start: 0.7544 (m-30) cc_final: 0.7244 (m-30) REVERT: B 78 ASN cc_start: 0.7595 (m110) cc_final: 0.7252 (t0) REVERT: B 187 MET cc_start: 0.8265 (mtm) cc_final: 0.7543 (ttt) outliers start: 18 outliers final: 11 residues processed: 84 average time/residue: 0.5275 time to fit residues: 46.1137 Evaluate side-chains 79 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.181 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 40 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 52 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.117639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099948 restraints weight = 5605.903| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 1.84 r_work: 0.3123 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2984 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3056 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= 0.158 Angle : 0.568 6.499 6172 Z= 0.291 Chirality : 0.043 0.149 670 Planarity : 0.004 0.047 775 Dihedral : 12.882 153.104 679 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % 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: 0.84 (0.36), residues: 545 helix: 1.65 (0.34), residues: 244 sheet: -1.21 (0.55), residues: 66 loop : 0.05 (0.40), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 189 TYR 0.011 0.001 TYR B 261 PHE 0.010 0.001 PHE A 599 TRP 0.009 0.001 TRP A 342 HIS 0.002 0.001 HIS A 477 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 4562) covalent geometry : angle 0.56807 / 0.29 ( 6172) hydrogen bonds : bond 0.03933 / 2.62 ( 208) hydrogen bonds : angle 4.91388 / 3.56 ( 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 95 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.111 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8111 (ptp) cc_final: 0.7825 (ptt) REVERT: A 609 LEU cc_start: 0.8489 (mt) cc_final: 0.8222 (mp) REVERT: B 67 ASP cc_start: 0.7576 (m-30) cc_final: 0.7252 (m-30) REVERT: B 78 ASN cc_start: 0.7596 (m110) cc_final: 0.7269 (t0) REVERT: B 187 MET cc_start: 0.8268 (mtm) cc_final: 0.7582 (ttt) outliers start: 19 outliers final: 10 residues processed: 89 average time/residue: 0.4583 time to fit residues: 42.4097 Evaluate side-chains 82 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 214 GLN 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: 0.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.117343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.099939 restraints weight = 5107.899| |-----------------------------------------------------------------------------| r_work (start): 0.3237 rms_B_bonded: 1.74 r_work: 0.3126 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3121 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= 0.172 Angle : 0.587 6.993 6172 Z= 0.299 Chirality : 0.043 0.152 670 Planarity : 0.004 0.046 775 Dihedral : 13.054 154.517 679 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.73 % Allowed : 16.80 % 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: 0.82 (0.36), residues: 545 helix: 1.57 (0.34), residues: 244 sheet: -0.92 (0.52), residues: 71 loop : 0.05 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 189 TYR 0.008 0.002 TYR B 261 PHE 0.011 0.001 PHE B 311 TRP 0.012 0.002 TRP A 342 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.17 ( 4562) covalent geometry : angle 0.58714 / 0.30 ( 6172) hydrogen bonds : bond 0.04032 / 2.69 ( 208) hydrogen bonds : angle 4.95598 / 3.58 ( 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 87 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8149 (ptp) cc_final: 0.7870 (ptt) REVERT: A 575 LYS cc_start: 0.8419 (OUTLIER) cc_final: 0.7876 (mtmm) REVERT: A 609 LEU cc_start: 0.8493 (mt) cc_final: 0.8228 (mp) REVERT: B 67 ASP cc_start: 0.7560 (m-30) cc_final: 0.7276 (m-30) REVERT: B 78 ASN cc_start: 0.7648 (m110) cc_final: 0.7319 (t0) REVERT: B 187 MET cc_start: 0.8264 (mtm) cc_final: 0.7611 (ttp) REVERT: B 240 TYR cc_start: 0.6672 (p90) cc_final: 0.6463 (p90) outliers start: 18 outliers final: 11 residues processed: 80 average time/residue: 0.4705 time to fit residues: 39.2484 Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.170 ------------------------------------------------------------------------------- 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 147 ASP 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: 1.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 42 optimal weight: 0.0270 chunk 24 optimal weight: 0.0980 chunk 19 optimal weight: 0.9990 chunk 49 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 overall best weight: 0.3096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.119890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.102276 restraints weight = 5409.062| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.85 r_work: 0.3156 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4562 Z= 0.120 Angle : 0.546 7.030 6172 Z= 0.279 Chirality : 0.042 0.141 670 Planarity : 0.004 0.047 775 Dihedral : 12.430 147.205 679 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 3.11 % Allowed : 17.01 % 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: 0.87 (0.36), residues: 545 helix: 1.66 (0.34), residues: 243 sheet: -1.22 (0.55), residues: 66 loop : 0.09 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 189 TYR 0.011 0.001 TYR B 261 PHE 0.009 0.001 PHE A 599 TRP 0.016 0.001 TRP A 342 HIS 0.003 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 4562) covalent geometry : angle 0.54612 / 0.28 ( 6172) hydrogen bonds : bond 0.03631 / 2.45 ( 208) hydrogen bonds : angle 4.81546 / 3.48 ( 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 94 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8075 (ptp) cc_final: 0.7782 (ptt) REVERT: A 575 LYS cc_start: 0.8428 (OUTLIER) cc_final: 0.7912 (mtmm) REVERT: A 609 LEU cc_start: 0.8482 (mt) cc_final: 0.8199 (mp) REVERT: B 67 ASP cc_start: 0.7547 (m-30) cc_final: 0.7244 (m-30) REVERT: B 78 ASN cc_start: 0.7660 (m110) cc_final: 0.7345 (t0) REVERT: B 187 MET cc_start: 0.8249 (mtm) cc_final: 0.7499 (ttt) outliers start: 15 outliers final: 9 residues processed: 87 average time/residue: 0.4729 time to fit residues: 42.9128 Evaluate side-chains 80 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 23 optimal weight: 0.0170 chunk 45 optimal weight: 2.9990 chunk 8 optimal weight: 0.0030 chunk 20 optimal weight: 0.3980 chunk 13 optimal weight: 0.3980 chunk 38 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 48 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 overall best weight: 0.2828 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.120472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.103062 restraints weight = 5393.920| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 1.80 r_work: 0.3170 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3336 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= 0.114 Angle : 0.540 6.795 6172 Z= 0.277 Chirality : 0.042 0.141 670 Planarity : 0.004 0.047 775 Dihedral : 12.318 145.915 679 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.11 % Allowed : 16.80 % 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: 0.87 (0.36), residues: 545 helix: 1.63 (0.34), residues: 244 sheet: -1.13 (0.55), residues: 65 loop : 0.10 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 189 TYR 0.011 0.001 TYR B 261 PHE 0.008 0.001 PHE A 599 TRP 0.018 0.001 TRP A 342 HIS 0.002 0.001 HIS A 460 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.11 ( 4562) covalent geometry : angle 0.53982 / 0.28 ( 6172) hydrogen bonds : bond 0.03556 / 2.40 ( 208) hydrogen bonds : angle 4.73025 / 3.42 ( 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: 15 poor density : 71 time to evaluate : 0.108 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8052 (ptp) cc_final: 0.7748 (ptt) REVERT: A 575 LYS cc_start: 0.8426 (OUTLIER) cc_final: 0.7885 (mtmm) REVERT: A 609 LEU cc_start: 0.8516 (mt) cc_final: 0.8230 (mp) REVERT: B 67 ASP cc_start: 0.7509 (m-30) cc_final: 0.7257 (m-30) REVERT: B 78 ASN cc_start: 0.7645 (m110) cc_final: 0.7353 (t0) REVERT: B 187 MET cc_start: 0.8235 (mtm) cc_final: 0.7458 (ttm) REVERT: B 230 MET cc_start: 0.8509 (mmm) cc_final: 0.8069 (mmt) outliers start: 15 outliers final: 11 residues processed: 80 average time/residue: 0.4836 time to fit residues: 40.3064 Evaluate side-chains 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.236 ------------------------------------------------------------------------------- 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 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: 1.9990 chunk 27 optimal weight: 0.0050 chunk 1 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 0.0470 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.4492 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.119711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.101809 restraints weight = 5575.600| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.89 r_work: 0.3150 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4562 Z= 0.132 Angle : 0.565 6.919 6172 Z= 0.289 Chirality : 0.042 0.145 670 Planarity : 0.004 0.047 775 Dihedral : 12.471 148.468 679 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.49 % Allowed : 17.63 % 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: 0.91 (0.36), residues: 545 helix: 1.64 (0.34), residues: 244 sheet: -1.13 (0.55), residues: 65 loop : 0.15 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 495 TYR 0.010 0.001 TYR B 261 PHE 0.008 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/Z covalent geometry : bond 0.00310 / 0.13 ( 4562) covalent geometry : angle 0.56544 / 0.29 ( 6172) hydrogen bonds : bond 0.03645 / 2.46 ( 208) hydrogen bonds : angle 4.75898 / 3.45 ( 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 86 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 412 MET cc_start: 0.8094 (ptp) cc_final: 0.7788 (ptt) REVERT: A 609 LEU cc_start: 0.8515 (mt) cc_final: 0.8222 (mp) REVERT: B 67 ASP cc_start: 0.7518 (m-30) cc_final: 0.7251 (m-30) REVERT: B 78 ASN cc_start: 0.7677 (m110) cc_final: 0.7373 (t0) REVERT: B 187 MET cc_start: 0.8241 (mtm) cc_final: 0.7432 (ttm) outliers start: 12 outliers final: 11 residues processed: 81 average time/residue: 0.5062 time to fit residues: 42.7432 Evaluate side-chains 81 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.177 ------------------------------------------------------------------------------- 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 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 27 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 40 optimal weight: 0.1980 chunk 42 optimal weight: 1.9990 chunk 24 optimal weight: 0.0010 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 153 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.119567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101917 restraints weight = 5438.690| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.85 r_work: 0.3148 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4562 Z= 0.135 Angle : 0.551 6.823 6172 Z= 0.284 Chirality : 0.042 0.146 670 Planarity : 0.004 0.047 775 Dihedral : 12.581 149.392 679 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 2.49 % Allowed : 17.63 % 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: 0.91 (0.36), residues: 545 helix: 1.61 (0.34), residues: 244 sheet: -1.10 (0.55), residues: 65 loop : 0.17 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 189 TYR 0.010 0.001 TYR B 261 PHE 0.009 0.001 PHE A 599 TRP 0.019 0.002 TRP A 342 HIS 0.002 0.001 HIS A 466 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 ( 4562) covalent geometry : angle 0.55093 / 0.28 ( 6172) hydrogen bonds : bond 0.03712 / 2.52 ( 208) hydrogen bonds : angle 4.77788 / 3.48 ( 603) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.72 seconds wall clock time: 29 minutes 33.08 seconds (1773.08 seconds total)