Starting phenix.real_space_refine on Tue Feb 3 17:16:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9irb_60808/02_2026/9irb_60808.cif Found real_map, /net/cci-nas-00/data/ceres_data/9irb_60808/02_2026/9irb_60808.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9irb_60808/02_2026/9irb_60808.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9irb_60808/02_2026/9irb_60808.map" model { file = "/net/cci-nas-00/data/ceres_data/9irb_60808/02_2026/9irb_60808.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9irb_60808/02_2026/9irb_60808.cif" } resolution = 3.15 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= 0.127 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 3541 2.51 5 N 882 2.21 5 O 972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 5423 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3620 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3620 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 449} Chain breaks: 2 Chain: "H" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 975 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "L" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 828 Classifications: {'peptide': 107} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 102} Time building chain proxies: 0.91, per 1000 atoms: 0.17 Number of scatterers: 5423 At special positions: 0 Unit cell: (70, 72, 124, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 972 8.00 N 882 7.00 C 3541 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 153 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 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: 0.33 Conformation dependent library (CDL) restraints added in 350.3 milliseconds 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1282 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 56.1% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 33 through 56 removed outlier: 3.672A pdb=" N CYS A 37 " --> pdb=" O ARG A 33 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU A 41 " --> pdb=" O CYS A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 64 Processing helix chain 'A' and resid 72 through 99 removed outlier: 4.108A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 101 through 118 Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'A' and resid 128 through 133 removed outlier: 3.986A pdb=" N LEU A 132 " --> pdb=" O THR A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 185 removed outlier: 4.172A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix removed outlier: 3.733A pdb=" N GLN A 182 " --> pdb=" O PHE A 178 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL A 183 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ASP A 185 " --> pdb=" O ASP A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 220 removed outlier: 4.471A pdb=" N ALA A 214 " --> pdb=" O LEU A 210 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N TYR A 215 " --> pdb=" O GLY A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 244 removed outlier: 4.053A pdb=" N ILE A 228 " --> pdb=" O THR A 224 " (cutoff:3.500A) Proline residue: A 229 - end of helix Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.249A pdb=" N THR A 258 " --> pdb=" O GLY A 254 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 328 removed outlier: 4.146A pdb=" N VAL A 315 " --> pdb=" O LYS A 311 " (cutoff:3.500A) Proline residue: A 323 - end of helix Processing helix chain 'A' and resid 328 through 348 removed outlier: 3.670A pdb=" N THR A 340 " --> pdb=" O PHE A 336 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 343 " --> pdb=" O GLN A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.706A pdb=" N THR A 370 " --> pdb=" O ALA A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 387 removed outlier: 3.584A pdb=" N LEU A 379 " --> pdb=" O VAL A 375 " (cutoff:3.500A) Proline residue: A 382 - end of helix Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 400 through 430 Processing helix chain 'A' and resid 450 through 453 Processing helix chain 'A' and resid 454 through 479 removed outlier: 3.641A pdb=" N LEU A 460 " --> pdb=" O PRO A 456 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE A 461 " --> pdb=" O GLN A 457 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER A 469 " --> pdb=" O GLU A 465 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 511 Processing helix chain 'A' and resid 531 through 559 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.648A pdb=" N ARG H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.920A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 434 through 439 Processing sheet with id=AA2, first strand: chain 'H' and resid 3 through 5 Processing sheet with id=AA3, first strand: chain 'H' and resid 45 through 51 removed outlier: 4.076A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N MET H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N MET H 34 " --> pdb=" O MET H 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 100 through 102 removed outlier: 3.756A pdb=" N TYR H 109 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 8.521A pdb=" N TYR H 102 " --> pdb=" O TRP H 107 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N TRP H 107 " --> pdb=" O TYR H 102 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.768A pdb=" N MET L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 19 through 24 removed outlier: 3.883A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) 325 hydrogen bonds defined for protein. 939 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: 0.63 Time building geometry restraints manager: 0.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1672 1.34 - 1.46: 1357 1.46 - 1.58: 2490 1.58 - 1.69: 0 1.69 - 1.81: 43 Bond restraints: 5562 Sorted by residual: bond pdb=" N ASN L 92 " pdb=" CA ASN L 92 " ideal model delta sigma weight residual 1.459 1.490 -0.032 1.28e-02 6.10e+03 6.13e+00 bond pdb=" N GLU A 432 " pdb=" CA GLU A 432 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.40e-02 5.10e+03 5.26e+00 bond pdb=" N SER A 346 " pdb=" CA SER A 346 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.19e-02 7.06e+03 4.63e+00 bond pdb=" N GLN L 27 " pdb=" CA GLN L 27 " ideal model delta sigma weight residual 1.457 1.485 -0.027 1.29e-02 6.01e+03 4.52e+00 bond pdb=" CA TRP A 452 " pdb=" C TRP A 452 " ideal model delta sigma weight residual 1.522 1.496 0.026 1.38e-02 5.25e+03 3.60e+00 ... (remaining 5557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 7350 1.45 - 2.90: 175 2.90 - 4.36: 28 4.36 - 5.81: 10 5.81 - 7.26: 2 Bond angle restraints: 7565 Sorted by residual: angle pdb=" O SER A 346 " pdb=" C SER A 346 " pdb=" N LEU A 347 " ideal model delta sigma weight residual 122.07 124.74 -2.67 1.03e+00 9.43e-01 6.74e+00 angle pdb=" CA LYS A 431 " pdb=" C LYS A 431 " pdb=" N GLU A 432 " ideal model delta sigma weight residual 119.80 116.57 3.23 1.34e+00 5.57e-01 5.80e+00 angle pdb=" N SER A 346 " pdb=" CA SER A 346 " pdb=" C SER A 346 " ideal model delta sigma weight residual 111.07 108.50 2.57 1.07e+00 8.73e-01 5.76e+00 angle pdb=" N GLU A 432 " pdb=" CA GLU A 432 " pdb=" C GLU A 432 " ideal model delta sigma weight residual 113.89 110.15 3.74 1.58e+00 4.01e-01 5.59e+00 angle pdb=" O LYS A 431 " pdb=" C LYS A 431 " pdb=" N GLU A 432 " ideal model delta sigma weight residual 121.64 124.33 -2.69 1.23e+00 6.61e-01 4.77e+00 ... (remaining 7560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 2756 17.99 - 35.98: 364 35.98 - 53.97: 93 53.97 - 71.96: 10 71.96 - 89.95: 8 Dihedral angle restraints: 3231 sinusoidal: 1223 harmonic: 2008 Sorted by residual: dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 153 " pdb=" CB CYS A 153 " ideal model delta sinusoidal sigma weight residual 93.00 144.10 -51.10 1 1.00e+01 1.00e-02 3.57e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 62.36 30.64 1 1.00e+01 1.00e-02 1.34e+01 dihedral pdb=" CA VAL A 430 " pdb=" C VAL A 430 " pdb=" N LYS A 431 " pdb=" CA LYS A 431 " ideal model delta harmonic sigma weight residual 180.00 162.19 17.81 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 3228 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 647 0.046 - 0.092: 168 0.092 - 0.137: 39 0.137 - 0.183: 2 0.183 - 0.229: 1 Chirality restraints: 857 Sorted by residual: chirality pdb=" CB THR A 176 " pdb=" CA THR A 176 " pdb=" OG1 THR A 176 " pdb=" CG2 THR A 176 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" CA THR A 176 " pdb=" N THR A 176 " pdb=" C THR A 176 " pdb=" CB THR A 176 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.17 2.00e-01 2.50e+01 7.64e-01 chirality pdb=" CA GLU A 432 " pdb=" N GLU A 432 " pdb=" C GLU A 432 " pdb=" CB GLU A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 854 not shown) Planarity restraints: 943 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 228 " -0.023 5.00e-02 4.00e+02 3.51e-02 1.98e+00 pdb=" N PRO A 229 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 229 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 229 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG H 40 " -0.023 5.00e-02 4.00e+02 3.45e-02 1.90e+00 pdb=" N PRO H 41 " 0.060 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS H 52 " 0.021 5.00e-02 4.00e+02 3.19e-02 1.62e+00 pdb=" N PRO H 53 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO H 53 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO H 53 " 0.018 5.00e-02 4.00e+02 ... (remaining 940 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 440 2.74 - 3.28: 5486 3.28 - 3.82: 9707 3.82 - 4.36: 11609 4.36 - 4.90: 20450 Nonbonded interactions: 47692 Sorted by model distance: nonbonded pdb=" O ASN L 77 " pdb=" NE2 GLN L 79 " model vdw 2.196 3.120 nonbonded pdb=" O SER H 85 " pdb=" OG SER H 85 " model vdw 2.248 3.040 nonbonded pdb=" OH TYR A 342 " pdb=" OG SER A 415 " model vdw 2.259 3.040 nonbonded pdb=" O SER H 77 " pdb=" OG SER H 77 " model vdw 2.278 3.040 nonbonded pdb=" OG1 THR A 438 " pdb=" O ASN L 92 " model vdw 2.287 3.040 ... (remaining 47687 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: 3.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.350 Find NCS groups from input model: 0.010 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:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 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 : 0.004 0.039 5565 Z= 0.184 Angle : 0.565 7.259 7571 Z= 0.309 Chirality : 0.042 0.229 857 Planarity : 0.004 0.035 943 Dihedral : 17.358 89.949 1940 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.35 % Allowed : 29.64 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: -0.50 (0.33), residues: 689 helix: 0.69 (0.27), residues: 361 sheet: -1.94 (0.51), residues: 88 loop : -1.12 (0.43), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 393 TYR 0.020 0.001 TYR L 91 PHE 0.015 0.001 PHE A 194 TRP 0.010 0.001 TRP A 197 HIS 0.004 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00401 ( 5562) covalent geometry : angle 0.56506 ( 7565) SS BOND : bond 0.00342 ( 3) SS BOND : angle 0.85789 ( 6) hydrogen bonds : bond 0.13453 ( 325) hydrogen bonds : angle 6.13878 ( 939) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.144 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.0689 time to fit residues: 4.2042 Evaluate side-chains 42 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 42 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.0770 chunk 5 optimal weight: 0.0870 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 0.0770 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.1074 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN L 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.138858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.111435 restraints weight = 5508.485| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.36 r_work: 0.3336 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5565 Z= 0.116 Angle : 0.509 6.605 7571 Z= 0.266 Chirality : 0.041 0.182 857 Planarity : 0.004 0.036 943 Dihedral : 4.288 18.305 750 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.25 % Allowed : 26.86 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.11 (0.33), residues: 689 helix: 1.31 (0.28), residues: 363 sheet: -1.37 (0.55), residues: 88 loop : -1.23 (0.42), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 102 TYR 0.010 0.001 TYR H 102 PHE 0.021 0.001 PHE H 64 TRP 0.008 0.001 TRP A 197 HIS 0.005 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 5562) covalent geometry : angle 0.50854 ( 7565) SS BOND : bond 0.00217 ( 3) SS BOND : angle 0.75843 ( 6) hydrogen bonds : bond 0.04058 ( 325) hydrogen bonds : angle 4.77548 ( 939) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.111 Fit side-chains REVERT: L 79 GLN cc_start: 0.8244 (mm-40) cc_final: 0.7907 (mm-40) outliers start: 13 outliers final: 6 residues processed: 45 average time/residue: 0.0404 time to fit residues: 2.6867 Evaluate side-chains 40 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 75 ILE Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 107 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 40 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 13 optimal weight: 0.9990 chunk 61 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 63 optimal weight: 0.8980 chunk 36 optimal weight: 0.0270 chunk 42 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.136023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.108386 restraints weight = 5455.511| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.38 r_work: 0.3295 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5565 Z= 0.151 Angle : 0.517 6.848 7571 Z= 0.269 Chirality : 0.041 0.187 857 Planarity : 0.004 0.036 943 Dihedral : 4.216 18.902 750 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.43 % Allowed : 26.69 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.11 (0.33), residues: 689 helix: 1.37 (0.28), residues: 363 sheet: -1.45 (0.52), residues: 95 loop : -1.28 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.010 0.001 TYR H 102 PHE 0.013 0.001 PHE A 194 TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5562) covalent geometry : angle 0.51660 ( 7565) SS BOND : bond 0.00262 ( 3) SS BOND : angle 0.86581 ( 6) hydrogen bonds : bond 0.03990 ( 325) hydrogen bonds : angle 4.68012 ( 939) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 38 time to evaluate : 0.117 Fit side-chains REVERT: L 70 ASP cc_start: 0.7341 (OUTLIER) cc_final: 0.7134 (m-30) REVERT: L 79 GLN cc_start: 0.8268 (mm-40) cc_final: 0.7931 (mm-40) outliers start: 14 outliers final: 8 residues processed: 49 average time/residue: 0.0557 time to fit residues: 3.9916 Evaluate side-chains 47 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 107 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 38 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.5980 chunk 3 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3441 r_free = 0.3441 target = 0.136091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.107366 restraints weight = 5482.264| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.49 r_work: 0.3275 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.0985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5565 Z= 0.143 Angle : 0.511 6.809 7571 Z= 0.265 Chirality : 0.041 0.196 857 Planarity : 0.004 0.035 943 Dihedral : 4.201 18.235 750 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.47 % Allowed : 24.96 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.20 (0.34), residues: 689 helix: 1.46 (0.28), residues: 363 sheet: -1.49 (0.52), residues: 95 loop : -1.25 (0.43), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.011 0.001 TYR H 102 PHE 0.016 0.001 PHE H 64 TRP 0.008 0.001 TRP H 47 HIS 0.004 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 5562) covalent geometry : angle 0.51014 ( 7565) SS BOND : bond 0.00264 ( 3) SS BOND : angle 0.88591 ( 6) hydrogen bonds : bond 0.03846 ( 325) hydrogen bonds : angle 4.62046 ( 939) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 38 time to evaluate : 0.192 Fit side-chains REVERT: H 63 ASN cc_start: 0.8435 (m-40) cc_final: 0.8153 (m-40) REVERT: L 70 ASP cc_start: 0.7382 (OUTLIER) cc_final: 0.7155 (m-30) REVERT: L 79 GLN cc_start: 0.8206 (mm-40) cc_final: 0.7812 (mm-40) outliers start: 20 outliers final: 9 residues processed: 55 average time/residue: 0.0549 time to fit residues: 4.2830 Evaluate side-chains 48 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 107 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 37 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 13 optimal weight: 0.4980 chunk 65 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.134062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.106015 restraints weight = 5605.868| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.43 r_work: 0.2949 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.0989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5565 Z= 0.177 Angle : 0.537 6.861 7571 Z= 0.279 Chirality : 0.042 0.200 857 Planarity : 0.004 0.036 943 Dihedral : 4.284 18.670 750 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.95 % Allowed : 25.13 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.08 (0.34), residues: 689 helix: 1.39 (0.28), residues: 362 sheet: -1.83 (0.49), residues: 105 loop : -1.13 (0.44), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.012 0.001 TYR H 102 PHE 0.014 0.001 PHE A 194 TRP 0.010 0.001 TRP H 47 HIS 0.015 0.002 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 5562) covalent geometry : angle 0.53617 ( 7565) SS BOND : bond 0.00307 ( 3) SS BOND : angle 1.00862 ( 6) hydrogen bonds : bond 0.03940 ( 325) hydrogen bonds : angle 4.67819 ( 939) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 38 time to evaluate : 0.182 Fit side-chains REVERT: H 6 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8563 (mm-40) REVERT: L 70 ASP cc_start: 0.7464 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: L 79 GLN cc_start: 0.8222 (mm-40) cc_final: 0.7825 (mm-40) outliers start: 17 outliers final: 11 residues processed: 52 average time/residue: 0.0709 time to fit residues: 5.0176 Evaluate side-chains 51 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 38 time to evaluate : 0.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 107 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 68 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 35 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 chunk 40 optimal weight: 0.4980 chunk 67 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 63 optimal weight: 0.0470 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 0.0570 chunk 39 optimal weight: 0.3980 overall best weight: 0.2596 ------------------------------------------------------------------------------- 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 = 0.3456 r_free = 0.3456 target = 0.137303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.109605 restraints weight = 5523.312| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 1.41 r_work: 0.3033 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5565 Z= 0.123 Angle : 0.499 6.733 7571 Z= 0.260 Chirality : 0.041 0.195 857 Planarity : 0.004 0.035 943 Dihedral : 4.200 18.265 750 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 3.47 % Allowed : 24.26 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.29 (0.34), residues: 689 helix: 1.53 (0.28), residues: 361 sheet: -1.43 (0.53), residues: 94 loop : -1.18 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.011 0.001 TYR H 102 PHE 0.014 0.001 PHE A 194 TRP 0.009 0.001 TRP H 47 HIS 0.008 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 5562) covalent geometry : angle 0.49849 ( 7565) SS BOND : bond 0.00280 ( 3) SS BOND : angle 0.99039 ( 6) hydrogen bonds : bond 0.03676 ( 325) hydrogen bonds : angle 4.56729 ( 939) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 41 time to evaluate : 0.196 Fit side-chains REVERT: L 70 ASP cc_start: 0.7305 (OUTLIER) cc_final: 0.7010 (m-30) REVERT: L 79 GLN cc_start: 0.8150 (mm-40) cc_final: 0.7787 (mm-40) outliers start: 20 outliers final: 13 residues processed: 58 average time/residue: 0.0487 time to fit residues: 4.0058 Evaluate side-chains 53 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 107 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 62 optimal weight: 0.2980 chunk 46 optimal weight: 0.0770 chunk 56 optimal weight: 0.5980 overall best weight: 0.4338 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.135741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.107705 restraints weight = 5569.331| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.43 r_work: 0.3006 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5565 Z= 0.151 Angle : 0.519 6.839 7571 Z= 0.268 Chirality : 0.041 0.197 857 Planarity : 0.004 0.036 943 Dihedral : 4.208 18.928 750 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % Rotamer: Outliers : 3.12 % Allowed : 25.13 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.27 (0.34), residues: 689 helix: 1.54 (0.28), residues: 362 sheet: -1.72 (0.51), residues: 105 loop : -1.06 (0.45), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.012 0.001 TYR H 102 PHE 0.015 0.001 PHE H 64 TRP 0.007 0.001 TRP H 47 HIS 0.007 0.001 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 5562) covalent geometry : angle 0.51906 ( 7565) SS BOND : bond 0.00258 ( 3) SS BOND : angle 0.86855 ( 6) hydrogen bonds : bond 0.03758 ( 325) hydrogen bonds : angle 4.58364 ( 939) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 39 time to evaluate : 0.117 Fit side-chains REVERT: L 70 ASP cc_start: 0.7410 (OUTLIER) cc_final: 0.7121 (m-30) REVERT: L 79 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7765 (mm-40) outliers start: 18 outliers final: 13 residues processed: 54 average time/residue: 0.0529 time to fit residues: 3.9071 Evaluate side-chains 51 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 37 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 371 MET Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 107 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 67 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 7 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.132984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.104808 restraints weight = 5553.540| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.43 r_work: 0.2979 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5565 Z= 0.194 Angle : 0.555 7.781 7571 Z= 0.286 Chirality : 0.043 0.206 857 Planarity : 0.004 0.036 943 Dihedral : 4.344 18.415 750 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.12 % Allowed : 25.30 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.15 (0.34), residues: 689 helix: 1.48 (0.28), residues: 361 sheet: -1.82 (0.49), residues: 105 loop : -1.14 (0.45), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 61 TYR 0.012 0.001 TYR L 49 PHE 0.016 0.001 PHE A 194 TRP 0.011 0.001 TRP H 47 HIS 0.012 0.002 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 5562) covalent geometry : angle 0.55448 ( 7565) SS BOND : bond 0.00348 ( 3) SS BOND : angle 0.98289 ( 6) hydrogen bonds : bond 0.03997 ( 325) hydrogen bonds : angle 4.70914 ( 939) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 37 time to evaluate : 0.175 Fit side-chains REVERT: H 6 GLN cc_start: 0.8849 (OUTLIER) cc_final: 0.8571 (mm-40) REVERT: H 63 ASN cc_start: 0.8418 (m-40) cc_final: 0.8188 (m-40) REVERT: L 70 ASP cc_start: 0.7492 (OUTLIER) cc_final: 0.7259 (m-30) REVERT: L 79 GLN cc_start: 0.8223 (mm-40) cc_final: 0.7841 (mm-40) outliers start: 18 outliers final: 13 residues processed: 52 average time/residue: 0.0790 time to fit residues: 5.4834 Evaluate side-chains 52 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 363 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 496 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 107 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 47 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 53 optimal weight: 0.0980 chunk 44 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.134098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.105383 restraints weight = 5526.170| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.48 r_work: 0.3244 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5565 Z= 0.160 Angle : 0.531 7.156 7571 Z= 0.274 Chirality : 0.042 0.202 857 Planarity : 0.004 0.036 943 Dihedral : 4.304 18.516 750 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.77 % Allowed : 25.30 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.16 (0.34), residues: 689 helix: 1.49 (0.28), residues: 361 sheet: -1.85 (0.50), residues: 105 loop : -1.11 (0.45), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.012 0.001 TYR H 102 PHE 0.015 0.001 PHE A 194 TRP 0.009 0.001 TRP H 47 HIS 0.014 0.002 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5562) covalent geometry : angle 0.53073 ( 7565) SS BOND : bond 0.00306 ( 3) SS BOND : angle 0.91804 ( 6) hydrogen bonds : bond 0.03834 ( 325) hydrogen bonds : angle 4.66198 ( 939) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 36 time to evaluate : 0.156 Fit side-chains REVERT: H 6 GLN cc_start: 0.8847 (OUTLIER) cc_final: 0.8611 (mm-40) REVERT: H 63 ASN cc_start: 0.8407 (m-40) cc_final: 0.8186 (m-40) REVERT: L 70 ASP cc_start: 0.7311 (OUTLIER) cc_final: 0.7033 (m-30) REVERT: L 79 GLN cc_start: 0.8211 (mm-40) cc_final: 0.7850 (mm-40) outliers start: 16 outliers final: 11 residues processed: 50 average time/residue: 0.0665 time to fit residues: 4.6353 Evaluate side-chains 48 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 35 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 19 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 20 optimal weight: 0.0980 chunk 12 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 2 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.0970 chunk 45 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.3156 ------------------------------------------------------------------------------- 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 = 0.3442 r_free = 0.3442 target = 0.135925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.107355 restraints weight = 5485.664| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.49 r_work: 0.3272 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.1230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5565 Z= 0.131 Angle : 0.513 7.750 7571 Z= 0.264 Chirality : 0.041 0.197 857 Planarity : 0.004 0.036 943 Dihedral : 4.241 18.613 750 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.77 % Allowed : 25.30 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.32 (0.34), residues: 689 helix: 1.58 (0.28), residues: 361 sheet: -1.51 (0.53), residues: 95 loop : -1.18 (0.43), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.011 0.001 TYR H 102 PHE 0.015 0.001 PHE A 194 TRP 0.007 0.001 TRP H 47 HIS 0.011 0.002 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5562) covalent geometry : angle 0.51241 ( 7565) SS BOND : bond 0.00254 ( 3) SS BOND : angle 0.81419 ( 6) hydrogen bonds : bond 0.03677 ( 325) hydrogen bonds : angle 4.57134 ( 939) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1378 Ramachandran restraints generated. 689 Oldfield, 0 Emsley, 689 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.188 Fit side-chains REVERT: H 6 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8581 (mm-40) REVERT: H 63 ASN cc_start: 0.8418 (m-40) cc_final: 0.8201 (m-40) REVERT: L 70 ASP cc_start: 0.7288 (OUTLIER) cc_final: 0.6967 (m-30) REVERT: L 79 GLN cc_start: 0.8122 (mm-40) cc_final: 0.7791 (mm-40) outliers start: 16 outliers final: 13 residues processed: 53 average time/residue: 0.0621 time to fit residues: 4.5963 Evaluate side-chains 52 residues out of total 577 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 37 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 379 LEU Chi-restraints excluded: chain A residue 412 VAL Chi-restraints excluded: chain A residue 464 SER Chi-restraints excluded: chain A residue 522 THR Chi-restraints excluded: chain H residue 6 GLN Chi-restraints excluded: chain H residue 17 SER Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 63 THR Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 81 GLU Chi-restraints excluded: chain L residue 103 ASN Chi-restraints excluded: chain L residue 107 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 69 random chunks: chunk 59 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 36 optimal weight: 0.0470 chunk 40 optimal weight: 0.5980 chunk 30 optimal weight: 0.0670 chunk 28 optimal weight: 0.7980 overall best weight: 0.4216 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.157161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.123867 restraints weight = 5376.371| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.10 r_work: 0.3196 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5565 Z= 0.148 Angle : 0.525 7.787 7571 Z= 0.270 Chirality : 0.041 0.198 857 Planarity : 0.004 0.036 943 Dihedral : 4.273 18.722 750 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 3.47 % Allowed : 24.61 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.67 % 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: 0.31 (0.34), residues: 689 helix: 1.57 (0.28), residues: 361 sheet: -1.44 (0.53), residues: 94 loop : -1.21 (0.43), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 102 TYR 0.011 0.001 TYR H 102 PHE 0.015 0.001 PHE A 194 TRP 0.008 0.001 TRP H 47 HIS 0.012 0.002 HIS A 445 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 5562) covalent geometry : angle 0.52423 ( 7565) SS BOND : bond 0.00303 ( 3) SS BOND : angle 0.85356 ( 6) hydrogen bonds : bond 0.03738 ( 325) hydrogen bonds : angle 4.57488 ( 939) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1360.25 seconds wall clock time: 24 minutes 6.80 seconds (1446.80 seconds total)