Starting phenix.real_space_refine on Tue Feb 3 16:45:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jxm_61868/02_2026/9jxm_61868.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jxm_61868/02_2026/9jxm_61868.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jxm_61868/02_2026/9jxm_61868.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jxm_61868/02_2026/9jxm_61868.map" model { file = "/net/cci-nas-00/data/ceres_data/9jxm_61868/02_2026/9jxm_61868.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jxm_61868/02_2026/9jxm_61868.cif" } resolution = 3.48 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= 0.005 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 21 5.16 5 C 3330 2.51 5 N 833 2.21 5 O 877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 5063 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 5053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 609, 5053 Classifications: {'peptide': 609} Link IDs: {'PTRANS': 20, 'TRANS': 588} Chain breaks: 1 Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 10 Unusual residues: {'PO4': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.99, per 1000 atoms: 0.20 Number of scatterers: 5063 At special positions: 0 Unit cell: (98.115, 71.74, 103.39, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 21 16.00 P 2 15.00 O 877 8.00 N 833 7.00 C 3330 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 415 " - pdb=" SG CYS B 440 " distance=2.02 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: 0.29 Conformation dependent library (CDL) restraints added in 276.4 milliseconds 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'B' and resid 3 through 10 Processing helix chain 'B' and resid 12 through 19 removed outlier: 3.525A pdb=" N ARG B 16 " --> pdb=" O PRO B 13 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LYS B 17 " --> pdb=" O GLU B 14 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N TYR B 19 " --> pdb=" O ARG B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 35 Processing helix chain 'B' and resid 43 through 99 removed outlier: 3.849A pdb=" N LYS B 99 " --> pdb=" O LEU B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 168 removed outlier: 3.546A pdb=" N LEU B 140 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER B 141 " --> pdb=" O GLU B 137 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N LYS B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 180 removed outlier: 3.522A pdb=" N ASP B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 183 No H-bonds generated for 'chain 'B' and resid 181 through 183' Processing helix chain 'B' and resid 190 through 205 Processing helix chain 'B' and resid 210 through 219 Processing helix chain 'B' and resid 223 through 227 removed outlier: 4.038A pdb=" N ALA B 226 " --> pdb=" O LEU B 223 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN B 227 " --> pdb=" O GLY B 224 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 227' Processing helix chain 'B' and resid 230 through 258 Processing helix chain 'B' and resid 265 through 272 Processing helix chain 'B' and resid 272 through 296 removed outlier: 3.502A pdb=" N PHE B 276 " --> pdb=" O TYR B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 303 removed outlier: 3.788A pdb=" N ILE B 302 " --> pdb=" O ASN B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 337 removed outlier: 3.713A pdb=" N LEU B 316 " --> pdb=" O SER B 312 " (cutoff:3.500A) Processing helix chain 'B' and resid 345 through 360 removed outlier: 3.751A pdb=" N LEU B 349 " --> pdb=" O TYR B 345 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 383 Processing helix chain 'B' and resid 390 through 403 removed outlier: 3.550A pdb=" N PHE B 394 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ASN B 401 " --> pdb=" O ALA B 397 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N SER B 402 " --> pdb=" O ASP B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 420 removed outlier: 4.149A pdb=" N LEU B 407 " --> pdb=" O LEU B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 471 Proline residue: B 455 - end of helix Processing helix chain 'B' and resid 473 through 478 removed outlier: 3.549A pdb=" N VAL B 478 " --> pdb=" O PHE B 474 " (cutoff:3.500A) Processing helix chain 'B' and resid 480 through 502 removed outlier: 3.791A pdb=" N THR B 486 " --> pdb=" O LYS B 482 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG B 502 " --> pdb=" O THR B 498 " (cutoff:3.500A) Processing helix chain 'B' and resid 506 through 531 removed outlier: 3.705A pdb=" N PHE B 510 " --> pdb=" O ASP B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 571 removed outlier: 3.668A pdb=" N TYR B 560 " --> pdb=" O LYS B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 583 removed outlier: 3.691A pdb=" N GLN B 576 " --> pdb=" O ALA B 572 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 622 Proline residue: B 598 - end of helix removed outlier: 3.790A pdb=" N PHE B 609 " --> pdb=" O PHE B 605 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE B 610 " --> pdb=" O VAL B 606 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN B 618 " --> pdb=" O ASN B 614 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ASN B 619 " --> pdb=" O GLU B 615 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY B 621 " --> pdb=" O LEU B 617 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLU B 622 " --> pdb=" O ASN B 618 " (cutoff:3.500A) 344 hydrogen bonds defined for protein. 1026 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: 0.53 Time building geometry restraints manager: 0.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.06 - 1.21: 6 1.21 - 1.36: 1577 1.36 - 1.51: 1816 1.51 - 1.66: 1777 1.66 - 1.81: 30 Bond restraints: 5206 Sorted by residual: bond pdb=" C ASP B 130 " pdb=" O ASP B 130 " ideal model delta sigma weight residual 1.235 1.064 0.171 1.25e-02 6.40e+03 1.87e+02 bond pdb=" C LEU B 131 " pdb=" O LEU B 131 " ideal model delta sigma weight residual 1.236 1.076 0.160 1.22e-02 6.72e+03 1.72e+02 bond pdb=" C LYS B 129 " pdb=" O LYS B 129 " ideal model delta sigma weight residual 1.236 1.072 0.163 1.29e-02 6.01e+03 1.61e+02 bond pdb=" C LYS B 129 " pdb=" N ASP B 130 " ideal model delta sigma weight residual 1.335 1.207 0.127 1.42e-02 4.96e+03 8.05e+01 bond pdb=" C ILE B 128 " pdb=" N LYS B 129 " ideal model delta sigma weight residual 1.334 1.225 0.109 1.38e-02 5.25e+03 6.28e+01 ... (remaining 5201 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 7000 3.18 - 6.37: 49 6.37 - 9.55: 7 9.55 - 12.74: 3 12.74 - 15.92: 1 Bond angle restraints: 7060 Sorted by residual: angle pdb=" C ASP B 130 " pdb=" CA ASP B 130 " pdb=" CB ASP B 130 " ideal model delta sigma weight residual 109.07 124.99 -15.92 1.68e+00 3.54e-01 8.98e+01 angle pdb=" N THR B 582 " pdb=" CA THR B 582 " pdb=" C THR B 582 " ideal model delta sigma weight residual 111.28 101.57 9.71 1.09e+00 8.42e-01 7.94e+01 angle pdb=" N ASP B 130 " pdb=" CA ASP B 130 " pdb=" C ASP B 130 " ideal model delta sigma weight residual 113.97 103.64 10.33 1.28e+00 6.10e-01 6.51e+01 angle pdb=" N LEU B 131 " pdb=" CA LEU B 131 " pdb=" CB LEU B 131 " ideal model delta sigma weight residual 110.20 120.04 -9.84 1.49e+00 4.50e-01 4.36e+01 angle pdb=" N SER B 578 " pdb=" CA SER B 578 " pdb=" C SER B 578 " ideal model delta sigma weight residual 111.40 104.38 7.02 1.22e+00 6.72e-01 3.32e+01 ... (remaining 7055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 2687 17.91 - 35.81: 291 35.81 - 53.72: 43 53.72 - 71.62: 6 71.62 - 89.53: 5 Dihedral angle restraints: 3032 sinusoidal: 1226 harmonic: 1806 Sorted by residual: dihedral pdb=" C ASP B 130 " pdb=" N ASP B 130 " pdb=" CA ASP B 130 " pdb=" CB ASP B 130 " ideal model delta harmonic sigma weight residual -122.60 -142.24 19.64 0 2.50e+00 1.60e-01 6.17e+01 dihedral pdb=" CA GLU B 436 " pdb=" C GLU B 436 " pdb=" N SER B 437 " pdb=" CA SER B 437 " ideal model delta harmonic sigma weight residual -180.00 -146.97 -33.03 0 5.00e+00 4.00e-02 4.36e+01 dihedral pdb=" N ASP B 130 " pdb=" C ASP B 130 " pdb=" CA ASP B 130 " pdb=" CB ASP B 130 " ideal model delta harmonic sigma weight residual 122.80 138.43 -15.63 0 2.50e+00 1.60e-01 3.91e+01 ... (remaining 3029 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.193: 764 0.193 - 0.386: 1 0.386 - 0.579: 2 0.579 - 0.772: 0 0.772 - 0.964: 1 Chirality restraints: 768 Sorted by residual: chirality pdb=" CA ASP B 130 " pdb=" N ASP B 130 " pdb=" C ASP B 130 " pdb=" CB ASP B 130 " both_signs ideal model delta sigma weight residual False 2.51 1.55 0.96 2.00e-01 2.50e+01 2.33e+01 chirality pdb=" CA LYS B 129 " pdb=" N LYS B 129 " pdb=" C LYS B 129 " pdb=" CB LYS B 129 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" CA LEU B 131 " pdb=" N LEU B 131 " pdb=" C LEU B 131 " pdb=" CB LEU B 131 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.79e+00 ... (remaining 765 not shown) Planarity restraints: 878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS B 129 " -0.025 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C LYS B 129 " 0.089 2.00e-02 2.50e+03 pdb=" O LYS B 129 " -0.035 2.00e-02 2.50e+03 pdb=" N ASP B 130 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 130 " -0.023 2.00e-02 2.50e+03 4.83e-02 2.33e+01 pdb=" C ASP B 130 " 0.084 2.00e-02 2.50e+03 pdb=" O ASP B 130 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU B 131 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 577 " -0.011 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C ILE B 577 " 0.042 2.00e-02 2.50e+03 pdb=" O ILE B 577 " -0.016 2.00e-02 2.50e+03 pdb=" N SER B 578 " -0.014 2.00e-02 2.50e+03 ... (remaining 875 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 79 2.64 - 3.21: 4901 3.21 - 3.77: 8094 3.77 - 4.34: 10596 4.34 - 4.90: 17382 Nonbonded interactions: 41052 Sorted by model distance: nonbonded pdb=" O THR B 580 " pdb=" CG2 THR B 583 " model vdw 2.078 3.460 nonbonded pdb=" O THR B 582 " pdb=" OG1 THR B 583 " model vdw 2.143 3.040 nonbonded pdb=" OD2 ASP B 130 " pdb=" O SER B 630 " model vdw 2.215 3.040 nonbonded pdb=" ND2 ASN B 432 " pdb=" OG SER B 434 " model vdw 2.240 3.120 nonbonded pdb=" NH2 ARG B 548 " pdb=" OE2 GLU B 613 " model vdw 2.334 3.120 ... (remaining 41047 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 1.350 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: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.150 Find NCS groups from input model: 0.020 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 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 : 0.008 0.171 5207 Z= 0.495 Angle : 0.732 15.921 7062 Z= 0.474 Chirality : 0.060 0.964 768 Planarity : 0.004 0.051 878 Dihedral : 14.772 89.529 1859 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.17 % Allowed : 7.27 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 13.52 % Favored : 86.48 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: -1.63 (0.31), residues: 605 helix: -0.12 (0.22), residues: 440 sheet: None (None), residues: 0 loop : -3.68 (0.42), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 502 TYR 0.015 0.001 TYR B 148 PHE 0.013 0.001 PHE B 610 TRP 0.010 0.001 TRP B 607 HIS 0.003 0.001 HIS B 163 Details of bonding type rmsd covalent geometry : bond 0.00813 ( 5206) covalent geometry : angle 0.73190 ( 7060) SS BOND : bond 0.00849 ( 1) SS BOND : angle 1.24753 ( 2) hydrogen bonds : bond 0.14551 ( 344) hydrogen bonds : angle 5.81924 ( 1026) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.166 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 167 LEU cc_start: 0.8853 (mp) cc_final: 0.8592 (mp) REVERT: B 352 TYR cc_start: 0.8268 (m-80) cc_final: 0.7878 (m-80) REVERT: B 360 ILE cc_start: 0.9321 (pt) cc_final: 0.8967 (mt) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0561 time to fit residues: 5.7741 Evaluate side-chains 53 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 58 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 33 GLN B 193 GLN B 288 ASN B 462 GLN B 587 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.139118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.103059 restraints weight = 8178.318| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.49 r_work: 0.3120 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5207 Z= 0.142 Angle : 0.552 7.751 7062 Z= 0.295 Chirality : 0.039 0.135 768 Planarity : 0.004 0.028 878 Dihedral : 4.841 32.998 669 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.79 % Favored : 94.05 % Rotamer: Outliers : 2.22 % Allowed : 14.44 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.30 (0.35), residues: 605 helix: 1.42 (0.24), residues: 440 sheet: None (None), residues: 0 loop : -3.34 (0.45), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 49 TYR 0.014 0.001 TYR B 148 PHE 0.015 0.001 PHE B 517 TRP 0.025 0.002 TRP B 573 HIS 0.003 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 5206) covalent geometry : angle 0.55210 ( 7060) SS BOND : bond 0.00417 ( 1) SS BOND : angle 0.61827 ( 2) hydrogen bonds : bond 0.04484 ( 344) hydrogen bonds : angle 4.02651 ( 1026) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8393 (t80) cc_final: 0.8096 (t80) REVERT: B 126 ARG cc_start: 0.8580 (mtt180) cc_final: 0.7957 (mtp85) REVERT: B 127 ASN cc_start: 0.8683 (t0) cc_final: 0.8251 (t0) REVERT: B 130 ASP cc_start: 0.8798 (OUTLIER) cc_final: 0.8386 (p0) REVERT: B 352 TYR cc_start: 0.8427 (m-80) cc_final: 0.7944 (m-80) REVERT: B 360 ILE cc_start: 0.9392 (pt) cc_final: 0.9116 (mt) REVERT: B 398 ASP cc_start: 0.8889 (OUTLIER) cc_final: 0.8688 (t0) REVERT: B 477 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9035 (mp) REVERT: B 496 TYR cc_start: 0.8479 (t80) cc_final: 0.8046 (t80) outliers start: 12 outliers final: 4 residues processed: 71 average time/residue: 0.0688 time to fit residues: 6.1760 Evaluate side-chains 63 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 477 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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 = 0.3780 r_free = 0.3780 target = 0.137368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.101980 restraints weight = 8223.514| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.42 r_work: 0.3101 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5207 Z= 0.158 Angle : 0.531 6.208 7062 Z= 0.284 Chirality : 0.039 0.127 768 Planarity : 0.003 0.027 878 Dihedral : 4.675 30.379 669 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 3.70 % Allowed : 13.89 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % 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: 0.97 (0.36), residues: 605 helix: 1.93 (0.24), residues: 440 sheet: None (None), residues: 0 loop : -3.17 (0.46), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 308 TYR 0.013 0.001 TYR B 148 PHE 0.016 0.001 PHE B 517 TRP 0.038 0.002 TRP B 573 HIS 0.004 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 5206) covalent geometry : angle 0.53065 ( 7060) SS BOND : bond 0.00448 ( 1) SS BOND : angle 0.80455 ( 2) hydrogen bonds : bond 0.04142 ( 344) hydrogen bonds : angle 3.77380 ( 1026) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.198 Fit side-chains REVERT: B 73 TYR cc_start: 0.8439 (t80) cc_final: 0.8162 (t80) REVERT: B 127 ASN cc_start: 0.8818 (t0) cc_final: 0.8206 (t0) REVERT: B 130 ASP cc_start: 0.8711 (OUTLIER) cc_final: 0.8239 (p0) REVERT: B 314 GLN cc_start: 0.8959 (OUTLIER) cc_final: 0.8238 (mt0) REVERT: B 352 TYR cc_start: 0.8518 (m-80) cc_final: 0.7950 (m-80) REVERT: B 496 TYR cc_start: 0.8503 (t80) cc_final: 0.8024 (t80) outliers start: 20 outliers final: 9 residues processed: 72 average time/residue: 0.0585 time to fit residues: 5.6108 Evaluate side-chains 59 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 48 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 551 ILE Chi-restraints excluded: chain B residue 629 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 31 optimal weight: 0.0980 chunk 2 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 0.0970 chunk 17 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.139492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.104407 restraints weight = 8234.373| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.47 r_work: 0.3141 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5207 Z= 0.118 Angle : 0.511 6.914 7062 Z= 0.273 Chirality : 0.038 0.120 768 Planarity : 0.003 0.028 878 Dihedral : 4.507 28.756 669 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 2.22 % Allowed : 16.85 % Favored : 80.93 % 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: 1.34 (0.36), residues: 605 helix: 2.23 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -3.13 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 624 TYR 0.012 0.001 TYR B 518 PHE 0.016 0.001 PHE B 517 TRP 0.051 0.002 TRP B 573 HIS 0.002 0.001 HIS B 441 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5206) covalent geometry : angle 0.51148 ( 7060) SS BOND : bond 0.00261 ( 1) SS BOND : angle 0.44418 ( 2) hydrogen bonds : bond 0.03765 ( 344) hydrogen bonds : angle 3.62029 ( 1026) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.199 Fit side-chains REVERT: B 73 TYR cc_start: 0.8457 (t80) cc_final: 0.8136 (t80) REVERT: B 126 ARG cc_start: 0.8539 (mtt180) cc_final: 0.7786 (mtp85) REVERT: B 127 ASN cc_start: 0.8750 (t0) cc_final: 0.8085 (t0) REVERT: B 130 ASP cc_start: 0.8571 (OUTLIER) cc_final: 0.8216 (p0) REVERT: B 496 TYR cc_start: 0.8436 (t80) cc_final: 0.8026 (t80) REVERT: B 507 THR cc_start: 0.7999 (OUTLIER) cc_final: 0.7734 (m) outliers start: 12 outliers final: 7 residues processed: 63 average time/residue: 0.0676 time to fit residues: 5.7291 Evaluate side-chains 59 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 130 ASP Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 507 THR Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 49 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 50 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.138129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.102230 restraints weight = 8338.052| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.52 r_work: 0.3124 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5207 Z= 0.131 Angle : 0.514 7.011 7062 Z= 0.271 Chirality : 0.038 0.122 768 Planarity : 0.003 0.029 878 Dihedral : 4.426 27.289 669 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.78 % Allowed : 16.85 % Favored : 80.37 % 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: 1.44 (0.36), residues: 605 helix: 2.31 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -3.11 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.014 0.001 TYR B 445 PHE 0.014 0.001 PHE B 610 TRP 0.066 0.002 TRP B 573 HIS 0.002 0.001 HIS B 476 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 5206) covalent geometry : angle 0.51418 ( 7060) SS BOND : bond 0.00336 ( 1) SS BOND : angle 0.67454 ( 2) hydrogen bonds : bond 0.03704 ( 344) hydrogen bonds : angle 3.58925 ( 1026) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8433 (t80) cc_final: 0.8155 (t80) REVERT: B 123 VAL cc_start: 0.7461 (OUTLIER) cc_final: 0.7104 (p) REVERT: B 126 ARG cc_start: 0.8532 (mtt180) cc_final: 0.7699 (mtp85) REVERT: B 127 ASN cc_start: 0.8729 (t0) cc_final: 0.8062 (t0) REVERT: B 130 ASP cc_start: 0.8517 (m-30) cc_final: 0.8121 (p0) REVERT: B 352 TYR cc_start: 0.8248 (m-80) cc_final: 0.7887 (m-80) outliers start: 15 outliers final: 10 residues processed: 66 average time/residue: 0.0495 time to fit residues: 4.5491 Evaluate side-chains 62 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 0.0870 chunk 58 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 46 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.138069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.101584 restraints weight = 8388.562| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.55 r_work: 0.3125 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5207 Z= 0.138 Angle : 0.513 7.367 7062 Z= 0.272 Chirality : 0.038 0.122 768 Planarity : 0.003 0.031 878 Dihedral : 4.381 25.977 669 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.96 % Allowed : 17.41 % Favored : 79.63 % 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: 1.50 (0.36), residues: 605 helix: 2.35 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -3.08 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.020 0.001 TYR B 445 PHE 0.014 0.001 PHE B 610 TRP 0.081 0.002 TRP B 573 HIS 0.002 0.001 HIS B 313 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 5206) covalent geometry : angle 0.51252 ( 7060) SS BOND : bond 0.00329 ( 1) SS BOND : angle 0.72248 ( 2) hydrogen bonds : bond 0.03729 ( 344) hydrogen bonds : angle 3.56175 ( 1026) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8453 (t80) cc_final: 0.8154 (t80) REVERT: B 123 VAL cc_start: 0.7453 (OUTLIER) cc_final: 0.7102 (p) REVERT: B 126 ARG cc_start: 0.8553 (mtt180) cc_final: 0.7973 (mtp85) REVERT: B 127 ASN cc_start: 0.8706 (t0) cc_final: 0.8041 (t0) REVERT: B 130 ASP cc_start: 0.8518 (m-30) cc_final: 0.8112 (p0) REVERT: B 259 LEU cc_start: 0.8476 (tp) cc_final: 0.8262 (tt) outliers start: 16 outliers final: 11 residues processed: 67 average time/residue: 0.0523 time to fit residues: 4.8968 Evaluate side-chains 63 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 469 ASP Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 0.6980 chunk 31 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.138766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.102674 restraints weight = 8214.956| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.51 r_work: 0.3135 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5207 Z= 0.122 Angle : 0.518 7.822 7062 Z= 0.276 Chirality : 0.037 0.119 768 Planarity : 0.003 0.037 878 Dihedral : 4.319 24.986 669 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.78 % Allowed : 17.96 % Favored : 79.26 % 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: 1.59 (0.36), residues: 605 helix: 2.40 (0.25), residues: 442 sheet: None (None), residues: 0 loop : -3.03 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 49 TYR 0.012 0.001 TYR B 352 PHE 0.015 0.001 PHE B 610 TRP 0.097 0.002 TRP B 573 HIS 0.001 0.000 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 5206) covalent geometry : angle 0.51838 ( 7060) SS BOND : bond 0.00251 ( 1) SS BOND : angle 0.58098 ( 2) hydrogen bonds : bond 0.03644 ( 344) hydrogen bonds : angle 3.51761 ( 1026) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.169 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8447 (t80) cc_final: 0.8180 (t80) REVERT: B 123 VAL cc_start: 0.7336 (OUTLIER) cc_final: 0.6958 (p) REVERT: B 126 ARG cc_start: 0.8566 (mtt180) cc_final: 0.8016 (mtp85) REVERT: B 127 ASN cc_start: 0.8684 (t0) cc_final: 0.8055 (t0) REVERT: B 130 ASP cc_start: 0.8484 (m-30) cc_final: 0.8113 (p0) REVERT: B 251 LEU cc_start: 0.8839 (mt) cc_final: 0.8416 (tt) REVERT: B 259 LEU cc_start: 0.8435 (tp) cc_final: 0.8206 (tt) outliers start: 15 outliers final: 11 residues processed: 64 average time/residue: 0.0563 time to fit residues: 5.0034 Evaluate side-chains 65 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 13 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 52 optimal weight: 0.0370 chunk 40 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 55 optimal weight: 0.8980 chunk 51 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.103648 restraints weight = 8324.095| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.56 r_work: 0.3158 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5207 Z= 0.118 Angle : 0.519 8.249 7062 Z= 0.274 Chirality : 0.037 0.117 768 Planarity : 0.003 0.041 878 Dihedral : 4.276 23.782 669 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.59 % Allowed : 17.96 % Favored : 79.44 % 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: 1.72 (0.36), residues: 605 helix: 2.48 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -2.90 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.012 0.001 TYR B 352 PHE 0.015 0.001 PHE B 610 TRP 0.107 0.003 TRP B 573 HIS 0.001 0.000 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00260 ( 5206) covalent geometry : angle 0.51878 ( 7060) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.48236 ( 2) hydrogen bonds : bond 0.03520 ( 344) hydrogen bonds : angle 3.45908 ( 1026) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8501 (t80) cc_final: 0.8172 (t80) REVERT: B 123 VAL cc_start: 0.7373 (OUTLIER) cc_final: 0.6994 (p) REVERT: B 126 ARG cc_start: 0.8503 (mtt180) cc_final: 0.8006 (mtp85) REVERT: B 130 ASP cc_start: 0.8484 (m-30) cc_final: 0.8119 (p0) REVERT: B 251 LEU cc_start: 0.8812 (mt) cc_final: 0.8408 (tt) REVERT: B 259 LEU cc_start: 0.8439 (tp) cc_final: 0.8184 (tt) REVERT: B 489 MET cc_start: 0.7897 (tpp) cc_final: 0.7257 (tpp) REVERT: B 496 TYR cc_start: 0.8372 (t80) cc_final: 0.7958 (t80) REVERT: B 518 TYR cc_start: 0.6929 (t80) cc_final: 0.6381 (t80) outliers start: 14 outliers final: 10 residues processed: 65 average time/residue: 0.0650 time to fit residues: 5.8214 Evaluate side-chains 65 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 7.9990 chunk 54 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 45 optimal weight: 0.0870 chunk 55 optimal weight: 0.5980 chunk 14 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 479 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.139955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104025 restraints weight = 8235.603| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.52 r_work: 0.3168 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5207 Z= 0.115 Angle : 0.513 8.374 7062 Z= 0.269 Chirality : 0.037 0.120 768 Planarity : 0.003 0.033 878 Dihedral : 4.191 22.683 669 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.78 % Allowed : 18.33 % Favored : 78.89 % 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: 1.79 (0.36), residues: 605 helix: 2.52 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -2.86 (0.47), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.011 0.001 TYR B 352 PHE 0.015 0.001 PHE B 610 TRP 0.085 0.002 TRP B 573 HIS 0.001 0.000 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 5206) covalent geometry : angle 0.51299 ( 7060) SS BOND : bond 0.00173 ( 1) SS BOND : angle 0.55407 ( 2) hydrogen bonds : bond 0.03482 ( 344) hydrogen bonds : angle 3.42714 ( 1026) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 55 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8488 (t80) cc_final: 0.8105 (t80) REVERT: B 123 VAL cc_start: 0.7295 (OUTLIER) cc_final: 0.6899 (p) REVERT: B 126 ARG cc_start: 0.8525 (mtt180) cc_final: 0.8241 (mtp85) REVERT: B 130 ASP cc_start: 0.8449 (m-30) cc_final: 0.7962 (t0) REVERT: B 251 LEU cc_start: 0.8815 (mt) cc_final: 0.8383 (tt) REVERT: B 372 PHE cc_start: 0.8643 (m-80) cc_final: 0.8420 (m-80) REVERT: B 489 MET cc_start: 0.7905 (tpp) cc_final: 0.7498 (tpp) outliers start: 15 outliers final: 11 residues processed: 68 average time/residue: 0.0482 time to fit residues: 4.5227 Evaluate side-chains 65 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 519 ILE Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 36 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 3 optimal weight: 5.9990 chunk 7 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.139131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.103156 restraints weight = 8283.750| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.50 r_work: 0.3148 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.3108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5207 Z= 0.142 Angle : 0.538 8.577 7062 Z= 0.285 Chirality : 0.038 0.129 768 Planarity : 0.003 0.035 878 Dihedral : 4.301 21.941 669 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.22 % Allowed : 19.44 % Favored : 78.33 % 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: 1.75 (0.36), residues: 605 helix: 2.47 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -2.78 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 49 TYR 0.013 0.001 TYR B 352 PHE 0.015 0.001 PHE B 517 TRP 0.060 0.002 TRP B 573 HIS 0.002 0.001 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5206) covalent geometry : angle 0.53746 ( 7060) SS BOND : bond 0.00193 ( 1) SS BOND : angle 0.69677 ( 2) hydrogen bonds : bond 0.03631 ( 344) hydrogen bonds : angle 3.48023 ( 1026) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 73 TYR cc_start: 0.8512 (t80) cc_final: 0.8132 (t80) REVERT: B 123 VAL cc_start: 0.7331 (OUTLIER) cc_final: 0.6929 (p) REVERT: B 126 ARG cc_start: 0.8546 (mtt180) cc_final: 0.8239 (mtp85) REVERT: B 130 ASP cc_start: 0.8433 (m-30) cc_final: 0.7980 (t0) REVERT: B 251 LEU cc_start: 0.8822 (mt) cc_final: 0.8412 (tt) REVERT: B 372 PHE cc_start: 0.8677 (m-80) cc_final: 0.8461 (m-80) REVERT: B 489 MET cc_start: 0.7828 (tpp) cc_final: 0.7368 (tpp) REVERT: B 518 TYR cc_start: 0.7038 (t80) cc_final: 0.6669 (t80) outliers start: 12 outliers final: 10 residues processed: 65 average time/residue: 0.0460 time to fit residues: 4.2407 Evaluate side-chains 63 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 253 LEU Chi-restraints excluded: chain B residue 341 VAL Chi-restraints excluded: chain B residue 344 THR Chi-restraints excluded: chain B residue 346 VAL Chi-restraints excluded: chain B residue 365 THR Chi-restraints excluded: chain B residue 370 SER Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 551 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 56 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.139966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.104039 restraints weight = 8345.663| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.53 r_work: 0.3173 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5207 Z= 0.125 Angle : 0.524 8.877 7062 Z= 0.274 Chirality : 0.037 0.118 768 Planarity : 0.003 0.046 878 Dihedral : 4.202 19.770 669 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 2.04 % Allowed : 20.00 % Favored : 77.96 % 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: 1.82 (0.36), residues: 605 helix: 2.52 (0.25), residues: 441 sheet: None (None), residues: 0 loop : -2.74 (0.48), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG B 49 TYR 0.013 0.001 TYR B 352 PHE 0.015 0.001 PHE B 610 TRP 0.029 0.001 TRP B 573 HIS 0.002 0.000 HIS B 387 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 5206) covalent geometry : angle 0.52428 ( 7060) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.53470 ( 2) hydrogen bonds : bond 0.03492 ( 344) hydrogen bonds : angle 3.43341 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1005.73 seconds wall clock time: 17 minutes 56.97 seconds (1076.97 seconds total)