Starting phenix.real_space_refine on Fri Aug 22 14:57:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bzy_16345/08_2025/8bzy_16345.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bzy_16345/08_2025/8bzy_16345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8bzy_16345/08_2025/8bzy_16345.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bzy_16345/08_2025/8bzy_16345.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bzy_16345/08_2025/8bzy_16345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bzy_16345/08_2025/8bzy_16345.map" } resolution = 3.24 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= 0.028 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: 6 Type Number sf(0) Gaussians P 1 5.49 5 S 31 5.16 5 C 2817 2.51 5 N 702 2.21 5 O 759 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4311 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 429, 3300 Classifications: {'peptide': 429} Link IDs: {'PTRANS': 9, 'TRANS': 419} Chain breaks: 2 Chain: "B" Number of atoms: 942 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 942 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "A" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 69 Unusual residues: {'PLC': 1, 'SZU': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Time building chain proxies: 1.18, per 1000 atoms: 0.27 Number of scatterers: 4311 At special positions: 0 Unit cell: (89.838, 87.885, 69.006, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 31 16.00 P 1 15.00 F 1 9.00 O 759 8.00 N 702 7.00 C 2817 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 0.25 Conformation dependent library (CDL) restraints added in 96.7 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1004 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 3 sheets defined 73.8% alpha, 13.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.563A pdb=" N LEU A 21 " --> pdb=" O ALA A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 54 Processing helix chain 'A' and resid 57 through 86 removed outlier: 3.808A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 Processing helix chain 'A' and resid 116 through 122 Processing helix chain 'A' and resid 125 through 164 removed outlier: 4.430A pdb=" N LEU A 129 " --> pdb=" O HIS A 125 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR A 130 " --> pdb=" O GLY A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 removed outlier: 3.730A pdb=" N VAL A 221 " --> pdb=" O CYS A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 235 removed outlier: 3.647A pdb=" N ALA A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N VAL A 235 " --> pdb=" O ALA A 232 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 235' Processing helix chain 'A' and resid 288 through 304 Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'A' and resid 330 through 336 Processing helix chain 'A' and resid 338 through 367 removed outlier: 3.958A pdb=" N ARG A 365 " --> pdb=" O THR A 361 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS A 366 " --> pdb=" O TRP A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 393 Processing helix chain 'A' and resid 451 through 484 removed outlier: 3.521A pdb=" N VAL A 455 " --> pdb=" O PRO A 451 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N SER A 471 " --> pdb=" O ILE A 467 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE A 472 " --> pdb=" O GLY A 468 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL A 484 " --> pdb=" O LEU A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 516 through 518 No H-bonds generated for 'chain 'A' and resid 516 through 518' Processing helix chain 'A' and resid 519 through 546 Processing helix chain 'B' and resid 61 through 65 removed outlier: 3.513A pdb=" N LYS B 65 " --> pdb=" O ASP B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 91 removed outlier: 3.735A pdb=" N THR B 91 " --> pdb=" O PRO B 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.119A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER B 120 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N GLU B 33 " --> pdb=" O LYS B 99 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 13 removed outlier: 6.119A pdb=" N GLY B 10 " --> pdb=" O THR B 118 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N SER B 120 " --> pdb=" O GLY B 10 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL B 12 " --> pdb=" O SER B 120 " (cutoff:3.500A) removed outlier: 5.791A pdb=" N TYR B 108 " --> pdb=" O ASP B 100 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N GLY B 102 " --> pdb=" O TRP B 106 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N TRP B 106 " --> pdb=" O GLY B 102 " (cutoff:3.500A) 347 hydrogen bonds defined for protein. 1017 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: 0.58 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 654 1.31 - 1.43: 1236 1.43 - 1.56: 2462 1.56 - 1.68: 2 1.68 - 1.81: 52 Bond restraints: 4406 Sorted by residual: bond pdb=" C1 SZU A 602 " pdb=" N1 SZU A 602 " ideal model delta sigma weight residual 1.347 1.450 -0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" C8 SZU A 602 " pdb=" N6 SZU A 602 " ideal model delta sigma weight residual 1.396 1.319 0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C1 SZU A 602 " pdb=" O1 SZU A 602 " ideal model delta sigma weight residual 1.233 1.184 0.049 2.00e-02 2.50e+03 6.11e+00 bond pdb=" C1 SZU A 602 " pdb=" C8 SZU A 602 " ideal model delta sigma weight residual 1.476 1.524 -0.048 2.00e-02 2.50e+03 5.65e+00 bond pdb=" C15 SZU A 602 " pdb=" N4 SZU A 602 " ideal model delta sigma weight residual 1.370 1.323 0.047 2.00e-02 2.50e+03 5.52e+00 ... (remaining 4401 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 5910 1.99 - 3.97: 69 3.97 - 5.96: 6 5.96 - 7.94: 1 7.94 - 9.93: 2 Bond angle restraints: 5988 Sorted by residual: angle pdb=" O3P PLC A 601 " pdb=" P PLC A 601 " pdb=" O4P PLC A 601 " ideal model delta sigma weight residual 93.62 103.55 -9.93 3.00e+00 1.11e-01 1.10e+01 angle pdb=" CA LEU A 503 " pdb=" CB LEU A 503 " pdb=" CG LEU A 503 " ideal model delta sigma weight residual 116.30 106.94 9.36 3.50e+00 8.16e-02 7.15e+00 angle pdb=" C11 SZU A 602 " pdb=" C10 SZU A 602 " pdb=" O2 SZU A 602 " ideal model delta sigma weight residual 117.54 125.10 -7.56 3.00e+00 1.11e-01 6.36e+00 angle pdb=" C GLY A 199 " pdb=" N SER A 200 " pdb=" CA SER A 200 " ideal model delta sigma weight residual 121.80 127.47 -5.67 2.44e+00 1.68e-01 5.41e+00 angle pdb=" N ALA B 104 " pdb=" CA ALA B 104 " pdb=" C ALA B 104 " ideal model delta sigma weight residual 110.97 113.44 -2.47 1.09e+00 8.42e-01 5.14e+00 ... (remaining 5983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.48: 2499 28.48 - 56.96: 50 56.96 - 85.43: 0 85.43 - 113.91: 2 113.91 - 142.39: 2 Dihedral angle restraints: 2553 sinusoidal: 979 harmonic: 1574 Sorted by residual: dihedral pdb=" C13 SZU A 602 " pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " pdb=" N4 SZU A 602 " ideal model delta sinusoidal sigma weight residual 286.49 144.10 142.39 1 3.00e+01 1.11e-03 1.91e+01 dihedral pdb=" C13 SZU A 602 " pdb=" C14 SZU A 602 " pdb=" C15 SZU A 602 " pdb=" N5 SZU A 602 " ideal model delta sinusoidal sigma weight residual 105.00 -35.33 140.33 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" O2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C2 PLC A 601 " pdb=" O3P PLC A 601 " ideal model delta sinusoidal sigma weight residual -55.71 54.64 -110.35 1 3.00e+01 1.11e-03 1.44e+01 ... (remaining 2550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 387 0.025 - 0.050: 193 0.050 - 0.075: 79 0.075 - 0.100: 29 0.100 - 0.125: 9 Chirality restraints: 697 Sorted by residual: chirality pdb=" CA VAL B 93 " pdb=" N VAL B 93 " pdb=" C VAL B 93 " pdb=" CB VAL B 93 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.91e-01 chirality pdb=" C2 PLC A 601 " pdb=" C1 PLC A 601 " pdb=" C3 PLC A 601 " pdb=" O2 PLC A 601 " both_signs ideal model delta sigma weight residual False -2.31 -2.44 0.12 2.00e-01 2.50e+01 3.73e-01 chirality pdb=" CA VAL B 79 " pdb=" N VAL B 79 " pdb=" C VAL B 79 " pdb=" CB VAL B 79 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.92e-01 ... (remaining 694 not shown) Planarity restraints: 725 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 155 " -0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C GLN A 155 " 0.033 2.00e-02 2.50e+03 pdb=" O GLN A 155 " -0.012 2.00e-02 2.50e+03 pdb=" N ARG A 156 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 525 " -0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C LEU A 525 " 0.030 2.00e-02 2.50e+03 pdb=" O LEU A 525 " -0.011 2.00e-02 2.50e+03 pdb=" N ILE A 526 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 527 " -0.008 2.00e-02 2.50e+03 1.60e-02 2.56e+00 pdb=" C SER A 527 " 0.028 2.00e-02 2.50e+03 pdb=" O SER A 527 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL A 528 " -0.009 2.00e-02 2.50e+03 ... (remaining 722 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1229 2.82 - 3.34: 4397 3.34 - 3.86: 7399 3.86 - 4.38: 8083 4.38 - 4.90: 14661 Nonbonded interactions: 35769 Sorted by model distance: nonbonded pdb=" O ALA B 52 " pdb=" NH1 ARG B 72 " model vdw 2.297 3.120 nonbonded pdb=" OG SER A 390 " pdb=" O SER A 454 " model vdw 2.339 3.040 nonbonded pdb=" O ASN A 86 " pdb=" NZ LYS A 236 " model vdw 2.361 3.120 nonbonded pdb=" O VAL B 29 " pdb=" NH2 ARG B 72 " model vdw 2.398 3.120 nonbonded pdb=" O LEU A 60 " pdb=" OH TYR A 133 " model vdw 2.407 3.040 ... (remaining 35764 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: 4.380 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 4.970 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:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7269 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.103 4407 Z= 0.217 Angle : 0.553 9.930 5990 Z= 0.274 Chirality : 0.037 0.125 697 Planarity : 0.004 0.026 725 Dihedral : 12.927 142.389 1546 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 2.42 % Allowed : 4.63 % Favored : 92.95 % 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 aren not related in a simple way. whole: 2.10 (0.37), residues: 541 helix: 2.49 (0.27), residues: 366 sheet: 0.15 (0.76), residues: 40 loop : -1.43 (0.54), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 178 TYR 0.008 0.001 TYR A 64 PHE 0.013 0.001 PHE A 295 TRP 0.008 0.001 TRP A 470 HIS 0.002 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 4406) covalent geometry : angle 0.55310 ( 5988) SS BOND : bond 0.00024 ( 1) SS BOND : angle 0.86762 ( 2) hydrogen bonds : bond 0.09715 ( 343) hydrogen bonds : angle 5.02957 ( 1017) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.111 Fit side-chains REVERT: B 103 MET cc_start: 0.9205 (ptt) cc_final: 0.8682 (ptp) outliers start: 11 outliers final: 8 residues processed: 47 average time/residue: 0.0767 time to fit residues: 4.6158 Evaluate side-chains 45 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 50 optimal weight: 0.0070 chunk 53 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 228 GLN B 13 GLN ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.134136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.103133 restraints weight = 4615.248| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.87 r_work: 0.2954 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.0846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4407 Z= 0.126 Angle : 0.455 8.230 5990 Z= 0.241 Chirality : 0.036 0.119 697 Planarity : 0.003 0.029 725 Dihedral : 10.513 85.420 652 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.64 % Allowed : 7.27 % Favored : 90.09 % 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 aren not related in a simple way. whole: 2.58 (0.36), residues: 541 helix: 2.88 (0.25), residues: 367 sheet: 0.24 (0.77), residues: 40 loop : -1.33 (0.54), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.018 0.001 TYR B 60 PHE 0.012 0.001 PHE A 295 TRP 0.008 0.001 TRP A 470 HIS 0.002 0.001 HIS A 43 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 4406) covalent geometry : angle 0.45466 ( 5988) SS BOND : bond 0.00069 ( 1) SS BOND : angle 0.72353 ( 2) hydrogen bonds : bond 0.03985 ( 343) hydrogen bonds : angle 4.10558 ( 1017) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.137 Fit side-chains REVERT: B 103 MET cc_start: 0.9186 (ptt) cc_final: 0.8942 (ptp) outliers start: 12 outliers final: 7 residues processed: 51 average time/residue: 0.0573 time to fit residues: 3.7746 Evaluate side-chains 47 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 21 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 chunk 25 optimal weight: 0.3980 chunk 2 optimal weight: 0.5980 chunk 48 optimal weight: 0.0980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.135190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.103724 restraints weight = 4556.357| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.90 r_work: 0.2961 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4407 Z= 0.117 Angle : 0.428 7.679 5990 Z= 0.228 Chirality : 0.036 0.117 697 Planarity : 0.003 0.030 725 Dihedral : 8.826 59.297 648 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.42 % Allowed : 8.15 % Favored : 89.43 % 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 aren not related in a simple way. whole: 2.79 (0.37), residues: 541 helix: 3.07 (0.26), residues: 367 sheet: 0.28 (0.80), residues: 40 loop : -1.34 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 19 TYR 0.018 0.001 TYR B 60 PHE 0.011 0.001 PHE A 295 TRP 0.011 0.001 TRP A 224 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 4406) covalent geometry : angle 0.42837 ( 5988) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.68150 ( 2) hydrogen bonds : bond 0.03769 ( 343) hydrogen bonds : angle 3.92545 ( 1017) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.086 Fit side-chains REVERT: B 103 MET cc_start: 0.9055 (ptt) cc_final: 0.8787 (ptp) outliers start: 11 outliers final: 9 residues processed: 49 average time/residue: 0.0647 time to fit residues: 4.0267 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 16 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 7 optimal weight: 0.4980 chunk 40 optimal weight: 0.0270 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 51 optimal weight: 0.6980 overall best weight: 0.3638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 77 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.136290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.105509 restraints weight = 4543.837| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.85 r_work: 0.2986 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4407 Z= 0.108 Angle : 0.411 7.176 5990 Z= 0.219 Chirality : 0.035 0.116 697 Planarity : 0.003 0.030 725 Dihedral : 8.074 54.344 647 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.42 % Allowed : 9.47 % Favored : 88.11 % 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 aren not related in a simple way. whole: 2.94 (0.37), residues: 541 helix: 3.18 (0.26), residues: 367 sheet: 0.27 (0.79), residues: 40 loop : -1.27 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 19 TYR 0.019 0.001 TYR B 60 PHE 0.011 0.001 PHE A 295 TRP 0.009 0.001 TRP A 224 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 4406) covalent geometry : angle 0.41118 ( 5988) SS BOND : bond 0.00134 ( 1) SS BOND : angle 0.57488 ( 2) hydrogen bonds : bond 0.03593 ( 343) hydrogen bonds : angle 3.83647 ( 1017) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.141 Fit side-chains REVERT: A 236 LYS cc_start: 0.6629 (ttmt) cc_final: 0.6408 (tttt) REVERT: B 19 ARG cc_start: 0.8412 (ttt90) cc_final: 0.8206 (ttt90) REVERT: B 103 MET cc_start: 0.9074 (ptt) cc_final: 0.8829 (ptp) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.0720 time to fit residues: 4.3765 Evaluate side-chains 48 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 47 optimal weight: 0.0050 chunk 22 optimal weight: 0.0870 chunk 20 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 overall best weight: 0.5372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 335 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.135233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.104201 restraints weight = 4588.634| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.88 r_work: 0.2965 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4407 Z= 0.123 Angle : 0.432 7.471 5990 Z= 0.229 Chirality : 0.036 0.116 697 Planarity : 0.003 0.031 725 Dihedral : 7.940 51.920 647 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.30 % Allowed : 9.47 % Favored : 87.22 % 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 aren not related in a simple way. whole: 2.87 (0.36), residues: 541 helix: 3.11 (0.25), residues: 367 sheet: 0.30 (0.79), residues: 40 loop : -1.25 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 19 TYR 0.018 0.001 TYR B 60 PHE 0.011 0.001 PHE A 295 TRP 0.008 0.001 TRP A 224 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4406) covalent geometry : angle 0.43189 ( 5988) SS BOND : bond 0.00096 ( 1) SS BOND : angle 0.66516 ( 2) hydrogen bonds : bond 0.03785 ( 343) hydrogen bonds : angle 3.87029 ( 1017) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.175 Fit side-chains REVERT: B 72 ARG cc_start: 0.7960 (OUTLIER) cc_final: 0.7703 (ttp-110) REVERT: B 103 MET cc_start: 0.9085 (ptt) cc_final: 0.8826 (ptp) outliers start: 15 outliers final: 9 residues processed: 51 average time/residue: 0.0692 time to fit residues: 4.4551 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 51 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 3 optimal weight: 0.0170 chunk 50 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 9 optimal weight: 0.0980 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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 = 0.134944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.103207 restraints weight = 4671.666| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.98 r_work: 0.2947 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2793 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4407 Z= 0.126 Angle : 0.444 7.928 5990 Z= 0.232 Chirality : 0.036 0.116 697 Planarity : 0.003 0.031 725 Dihedral : 7.846 53.255 647 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.08 % Allowed : 10.13 % Favored : 86.78 % 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 aren not related in a simple way. whole: 2.87 (0.36), residues: 541 helix: 3.10 (0.26), residues: 367 sheet: 0.26 (0.79), residues: 40 loop : -1.21 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 19 TYR 0.018 0.001 TYR B 60 PHE 0.011 0.001 PHE A 295 TRP 0.007 0.001 TRP A 224 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 4406) covalent geometry : angle 0.44434 ( 5988) SS BOND : bond 0.00097 ( 1) SS BOND : angle 0.63375 ( 2) hydrogen bonds : bond 0.03797 ( 343) hydrogen bonds : angle 3.89463 ( 1017) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 39 time to evaluate : 0.148 Fit side-chains REVERT: B 38 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6619 (ptm160) REVERT: B 72 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.6955 (ptm160) REVERT: B 103 MET cc_start: 0.9027 (ptt) cc_final: 0.8777 (ptp) outliers start: 14 outliers final: 9 residues processed: 49 average time/residue: 0.0811 time to fit residues: 5.0053 Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 39 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.132995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.102044 restraints weight = 4627.085| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.88 r_work: 0.2936 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4407 Z= 0.148 Angle : 0.464 8.279 5990 Z= 0.244 Chirality : 0.037 0.117 697 Planarity : 0.003 0.031 725 Dihedral : 7.950 56.083 647 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.30 % Allowed : 9.91 % Favored : 86.78 % 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 aren not related in a simple way. whole: 2.77 (0.36), residues: 541 helix: 3.00 (0.26), residues: 367 sheet: 0.33 (0.81), residues: 40 loop : -1.21 (0.53), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.016 0.001 TYR B 60 PHE 0.012 0.001 PHE A 295 TRP 0.008 0.001 TRP A 470 HIS 0.002 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 4406) covalent geometry : angle 0.46402 ( 5988) SS BOND : bond 0.00018 ( 1) SS BOND : angle 0.86868 ( 2) hydrogen bonds : bond 0.04032 ( 343) hydrogen bonds : angle 3.98115 ( 1017) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 40 time to evaluate : 0.145 Fit side-chains REVERT: B 38 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.6738 (ptm160) REVERT: B 72 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.6955 (ptm160) REVERT: B 103 MET cc_start: 0.9077 (ptt) cc_final: 0.8836 (ptp) outliers start: 15 outliers final: 10 residues processed: 51 average time/residue: 0.0789 time to fit residues: 4.9237 Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 31 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 41 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 chunk 53 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 228 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.132353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.100799 restraints weight = 4644.305| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.95 r_work: 0.2915 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.1476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4407 Z= 0.156 Angle : 0.473 8.355 5990 Z= 0.249 Chirality : 0.037 0.117 697 Planarity : 0.003 0.031 725 Dihedral : 7.997 57.819 647 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.52 % Allowed : 10.13 % Favored : 86.34 % 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 aren not related in a simple way. whole: 2.73 (0.36), residues: 541 helix: 2.97 (0.25), residues: 366 sheet: 0.35 (0.81), residues: 40 loop : -1.19 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.016 0.001 TYR B 60 PHE 0.012 0.001 PHE A 295 TRP 0.010 0.001 TRP A 224 HIS 0.002 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 4406) covalent geometry : angle 0.47264 ( 5988) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.72314 ( 2) hydrogen bonds : bond 0.04095 ( 343) hydrogen bonds : angle 4.02083 ( 1017) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 38 time to evaluate : 0.091 Fit side-chains REVERT: B 38 ARG cc_start: 0.7223 (OUTLIER) cc_final: 0.6670 (ptm160) REVERT: B 72 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6909 (ptm160) REVERT: B 103 MET cc_start: 0.9025 (ptt) cc_final: 0.8787 (ptp) outliers start: 16 outliers final: 11 residues processed: 52 average time/residue: 0.0775 time to fit residues: 4.9666 Evaluate side-chains 50 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 37 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 385 ILE Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 18 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 17 optimal weight: 0.0970 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 37 optimal weight: 0.5980 chunk 53 optimal weight: 6.9990 chunk 52 optimal weight: 0.3980 chunk 7 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.135072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.104222 restraints weight = 4623.714| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 1.88 r_work: 0.2964 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4407 Z= 0.117 Angle : 0.444 7.643 5990 Z= 0.234 Chirality : 0.036 0.115 697 Planarity : 0.003 0.031 725 Dihedral : 7.752 58.506 647 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.86 % Allowed : 10.57 % Favored : 86.56 % 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 aren not related in a simple way. whole: 2.95 (0.36), residues: 541 helix: 3.15 (0.26), residues: 366 sheet: 0.45 (0.80), residues: 40 loop : -1.13 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.017 0.001 TYR B 60 PHE 0.011 0.001 PHE A 295 TRP 0.010 0.001 TRP A 224 HIS 0.002 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 4406) covalent geometry : angle 0.44433 ( 5988) SS BOND : bond 0.00104 ( 1) SS BOND : angle 0.50193 ( 2) hydrogen bonds : bond 0.03770 ( 343) hydrogen bonds : angle 3.91727 ( 1017) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 39 time to evaluate : 0.144 Fit side-chains REVERT: B 38 ARG cc_start: 0.7243 (OUTLIER) cc_final: 0.6697 (ptm160) REVERT: B 72 ARG cc_start: 0.7931 (OUTLIER) cc_final: 0.6930 (ptm160) outliers start: 13 outliers final: 9 residues processed: 48 average time/residue: 0.0769 time to fit residues: 4.5386 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 11 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 17 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.133595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.102616 restraints weight = 4600.892| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.87 r_work: 0.2940 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4407 Z= 0.145 Angle : 0.474 8.069 5990 Z= 0.248 Chirality : 0.037 0.116 697 Planarity : 0.003 0.031 725 Dihedral : 7.866 59.557 647 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.42 % Allowed : 11.23 % Favored : 86.34 % 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 aren not related in a simple way. whole: 2.79 (0.36), residues: 541 helix: 3.01 (0.25), residues: 366 sheet: 0.38 (0.80), residues: 40 loop : -1.15 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.019 0.001 TYR B 60 PHE 0.012 0.001 PHE A 295 TRP 0.010 0.001 TRP A 224 HIS 0.002 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4406) covalent geometry : angle 0.47420 ( 5988) SS BOND : bond 0.00077 ( 1) SS BOND : angle 0.64453 ( 2) hydrogen bonds : bond 0.03990 ( 343) hydrogen bonds : angle 3.98581 ( 1017) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1082 Ramachandran restraints generated. 541 Oldfield, 0 Emsley, 541 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.161 Fit side-chains REVERT: B 38 ARG cc_start: 0.7213 (OUTLIER) cc_final: 0.6666 (ptm160) REVERT: B 72 ARG cc_start: 0.7965 (OUTLIER) cc_final: 0.6971 (ptm160) outliers start: 11 outliers final: 9 residues processed: 46 average time/residue: 0.0692 time to fit residues: 4.0108 Evaluate side-chains 49 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 LEU Chi-restraints excluded: chain A residue 222 LEU Chi-restraints excluded: chain A residue 328 THR Chi-restraints excluded: chain A residue 352 THR Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain B residue 4 LEU Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 VAL Chi-restraints excluded: chain B residue 72 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 33 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 17 optimal weight: 0.1980 chunk 51 optimal weight: 0.9990 chunk 13 optimal weight: 3.9990 chunk 29 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.133637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.101894 restraints weight = 4649.976| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.98 r_work: 0.2928 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2775 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4407 Z= 0.145 Angle : 0.484 8.117 5990 Z= 0.251 Chirality : 0.037 0.116 697 Planarity : 0.003 0.031 725 Dihedral : 7.859 59.314 647 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.86 % Allowed : 10.79 % Favored : 86.34 % 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 aren not related in a simple way. whole: 2.78 (0.36), residues: 541 helix: 3.00 (0.25), residues: 366 sheet: 0.40 (0.81), residues: 40 loop : -1.14 (0.53), residues: 135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 19 TYR 0.019 0.001 TYR B 60 PHE 0.012 0.001 PHE A 295 TRP 0.009 0.001 TRP A 224 HIS 0.002 0.001 HIS A 507 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 4406) covalent geometry : angle 0.48404 ( 5988) SS BOND : bond 0.00083 ( 1) SS BOND : angle 0.63492 ( 2) hydrogen bonds : bond 0.04002 ( 343) hydrogen bonds : angle 3.98878 ( 1017) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1089.75 seconds wall clock time: 19 minutes 20.44 seconds (1160.44 seconds total)