Starting phenix.real_space_refine on Tue Aug 4 16:07:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rh9_53962/08_2026/9rh9_53962.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rh9_53962/08_2026/9rh9_53962.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rh9_53962/08_2026/9rh9_53962.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rh9_53962/08_2026/9rh9_53962.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rh9_53962/08_2026/9rh9_53962.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rh9_53962/08_2026/9rh9_53962.map" } resolution = 3.1 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= 0.002 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 19 5.16 5 C 3019 2.51 5 N 757 2.21 5 O 837 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4632 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2909 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 2909 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 15, 'TRANS': 371} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 816 Classifications: {'peptide': 106} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 101} Time building chain proxies: 0.83, per 1000 atoms: 0.18 Number of scatterers: 4632 At special positions: 0 Unit cell: (66.96, 77.004, 102.114, 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 19 16.00 O 837 8.00 N 757 7.00 C 3019 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 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: 0.22 Conformation dependent library (CDL) restraints added in 106.6 milliseconds 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1110 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 7 sheets defined 52.7% alpha, 19.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'A' and resid 12 through 31 removed outlier: 3.792A pdb=" N LEU A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 43 removed outlier: 4.784A pdb=" N GLY A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 5.702A pdb=" N TRP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 86 removed outlier: 3.651A pdb=" N ALA A 69 " --> pdb=" O ASP A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 89 No H-bonds generated for 'chain 'A' and resid 87 through 89' Processing helix chain 'A' and resid 90 through 117 removed outlier: 5.217A pdb=" N PHE A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Proline residue: A 97 - end of helix Proline residue: A 108 - end of helix removed outlier: 3.823A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 126 removed outlier: 3.546A pdb=" N TRP A 126 " --> pdb=" O ARG A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 145 removed outlier: 3.901A pdb=" N LEU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.527A pdb=" N LYS A 153 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 201 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.790A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.915A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N VAL A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 262 Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 262 through 272 Processing helix chain 'A' and resid 282 through 285 Processing helix chain 'A' and resid 286 through 298 Processing helix chain 'A' and resid 298 through 314 Processing helix chain 'A' and resid 324 through 335 removed outlier: 3.576A pdb=" N VAL A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 383 removed outlier: 3.556A pdb=" N VAL A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 32 removed outlier: 3.577A pdb=" N ASP B 31 " --> pdb=" O THR B 28 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N TYR B 32 " --> pdb=" O PHE B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 32' Processing helix chain 'C' and resid 79 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 45 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.521A pdb=" N VAL B 18 " --> pdb=" O LEU B 83 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.365A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.832A pdb=" N CYS B 96 " --> pdb=" O TRP B 108 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N TRP B 108 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LYS B 98 " --> pdb=" O ASP B 106 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.719A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.719A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) 292 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.53 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 728 1.32 - 1.44: 1271 1.44 - 1.56: 2706 1.56 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4736 Sorted by residual: bond pdb=" C GLU A 78 " pdb=" O GLU A 78 " ideal model delta sigma weight residual 1.236 1.196 0.040 1.29e-02 6.01e+03 9.57e+00 bond pdb=" N LEU A 4 " pdb=" CA LEU A 4 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.90e+00 bond pdb=" N ASP A 163 " pdb=" CA ASP A 163 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.37e+00 bond pdb=" N ASP A 164 " pdb=" CA ASP A 164 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.19e-02 7.06e+03 5.90e+00 bond pdb=" N HIS A 5 " pdb=" CA HIS A 5 " ideal model delta sigma weight residual 1.460 1.490 -0.031 1.45e-02 4.76e+03 4.53e+00 ... (remaining 4731 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 6201 1.30 - 2.60: 191 2.60 - 3.90: 36 3.90 - 5.20: 11 5.20 - 6.51: 2 Bond angle restraints: 6441 Sorted by residual: angle pdb=" N HIS A 3 " pdb=" CA HIS A 3 " pdb=" C HIS A 3 " ideal model delta sigma weight residual 108.31 113.65 -5.34 1.52e+00 4.33e-01 1.23e+01 angle pdb=" N HIS A 5 " pdb=" CA HIS A 5 " pdb=" C HIS A 5 " ideal model delta sigma weight residual 110.44 106.39 4.05 1.20e+00 6.94e-01 1.14e+01 angle pdb=" N LEU A 4 " pdb=" CA LEU A 4 " pdb=" CB LEU A 4 " ideal model delta sigma weight residual 110.49 115.39 -4.90 1.69e+00 3.50e-01 8.41e+00 angle pdb=" CA ASP A 163 " pdb=" CB ASP A 163 " pdb=" CG ASP A 163 " ideal model delta sigma weight residual 112.60 115.38 -2.78 1.00e+00 1.00e+00 7.73e+00 angle pdb=" CA HIS A 3 " pdb=" CB HIS A 3 " pdb=" CG HIS A 3 " ideal model delta sigma weight residual 113.80 116.52 -2.72 1.00e+00 1.00e+00 7.38e+00 ... (remaining 6436 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.58: 2503 17.58 - 35.16: 210 35.16 - 52.74: 45 52.74 - 70.31: 9 70.31 - 87.89: 5 Dihedral angle restraints: 2772 sinusoidal: 1031 harmonic: 1741 Sorted by residual: dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 55.72 37.28 1 1.00e+01 1.00e-02 1.96e+01 dihedral pdb=" CA GLU B 99 " pdb=" C GLU B 99 " pdb=" N GLU B 100 " pdb=" CA GLU B 100 " ideal model delta harmonic sigma weight residual 180.00 161.59 18.41 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA ASN B 103 " pdb=" C ASN B 103 " pdb=" N ASP B 104 " pdb=" CA ASP B 104 " ideal model delta harmonic sigma weight residual 180.00 162.23 17.77 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 570 0.038 - 0.075: 140 0.075 - 0.112: 35 0.112 - 0.150: 15 0.150 - 0.187: 1 Chirality restraints: 761 Sorted by residual: chirality pdb=" CA LYS A 2 " pdb=" N LYS A 2 " pdb=" C LYS A 2 " pdb=" CB LYS A 2 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CA PRO A 355 " pdb=" N PRO A 355 " pdb=" C PRO A 355 " pdb=" CB PRO A 355 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE A 55 " pdb=" N ILE A 55 " pdb=" C ILE A 55 " pdb=" CB ILE A 55 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.63e-01 ... (remaining 758 not shown) Planarity restraints: 793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 354 " -0.041 5.00e-02 4.00e+02 6.13e-02 6.02e+00 pdb=" N PRO A 355 " 0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 355 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 355 " -0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS A 3 " 0.010 2.00e-02 2.50e+03 2.15e-02 4.61e+00 pdb=" C HIS A 3 " -0.037 2.00e-02 2.50e+03 pdb=" O HIS A 3 " 0.014 2.00e-02 2.50e+03 pdb=" N LEU A 4 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 264 " -0.017 5.00e-02 4.00e+02 2.54e-02 1.03e+00 pdb=" N PRO A 265 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " -0.014 5.00e-02 4.00e+02 ... (remaining 790 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1190 2.80 - 3.32: 4569 3.32 - 3.85: 7583 3.85 - 4.37: 9077 4.37 - 4.90: 15663 Nonbonded interactions: 38082 Sorted by model distance: nonbonded pdb=" OG SER A 183 " pdb=" O ALA A 218 " model vdw 2.274 3.040 nonbonded pdb=" NE2 GLN C 6 " pdb=" OG1 THR C 102 " model vdw 2.297 3.120 nonbonded pdb=" O PRO C 8 " pdb=" OG1 THR C 102 " model vdw 2.347 3.040 nonbonded pdb=" O SER B 7 " pdb=" OG1 THR B 112 " model vdw 2.363 3.040 nonbonded pdb=" OH TYR A 38 " pdb=" O PHE A 269 " model vdw 2.390 3.040 ... (remaining 38077 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: 0.980 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 4.360 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:1.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 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 0.045 4738 Z= 0.182 Angle : 0.576 6.506 6445 Z= 0.335 Chirality : 0.039 0.187 761 Planarity : 0.003 0.061 793 Dihedral : 14.164 87.893 1656 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.20 % Allowed : 12.42 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.35), residues: 605 helix: 1.58 (0.32), residues: 278 sheet: 0.44 (0.44), residues: 131 loop : -0.24 (0.45), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 81 TYR 0.008 0.001 TYR C 49 PHE 0.012 0.001 PHE A 72 TRP 0.005 0.001 TRP A 216 HIS 0.006 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.18 ( 4736) covalent geometry : angle 0.57585 / 0.34 ( 6441) SS BOND : bond 0.00272 / 0.13 ( 2) SS BOND : angle 0.20631 / 0.11 ( 4) hydrogen bonds : bond 0.20741 / 14.22 ( 283) hydrogen bonds : angle 8.06408 / 5.90 ( 816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 0.097 Fit side-chains REVERT: A 11 ASP cc_start: 0.6698 (p0) cc_final: 0.6398 (p0) REVERT: A 49 ARG cc_start: 0.7672 (ttt-90) cc_final: 0.7277 (mtm-85) REVERT: A 240 LYS cc_start: 0.8619 (tttp) cc_final: 0.7258 (mptt) REVERT: A 329 MET cc_start: 0.7893 (mtt) cc_final: 0.7585 (mtp) REVERT: A 379 TRP cc_start: 0.7660 (m-10) cc_final: 0.7307 (m-10) outliers start: 1 outliers final: 1 residues processed: 80 average time/residue: 0.0727 time to fit residues: 7.1716 Evaluate side-chains 66 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 116 ASN A 225 HIS A 256 HIS A 359 ASN C 6 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.183207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.108449 restraints weight = 5411.026| |-----------------------------------------------------------------------------| r_work (start): 0.3044 rms_B_bonded: 2.55 r_work: 0.2897 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4738 Z= 0.183 Angle : 0.645 10.487 6445 Z= 0.326 Chirality : 0.043 0.158 761 Planarity : 0.004 0.034 793 Dihedral : 5.030 53.774 653 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.46 % Allowed : 12.02 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.34), residues: 605 helix: 1.78 (0.31), residues: 286 sheet: 0.57 (0.43), residues: 131 loop : -0.31 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 49 TYR 0.013 0.001 TYR C 49 PHE 0.016 0.002 PHE A 72 TRP 0.012 0.001 TRP B 36 HIS 0.007 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 ( 4736) covalent geometry : angle 0.64462 / 0.33 ( 6441) SS BOND : bond 0.00294 / 0.14 ( 2) SS BOND : angle 0.50042 / 0.23 ( 4) hydrogen bonds : bond 0.04177 / 3.06 ( 283) hydrogen bonds : angle 5.48698 / 4.02 ( 816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 59 time to evaluate : 0.172 Fit side-chains REVERT: A 28 MET cc_start: 0.8357 (mmm) cc_final: 0.8115 (mtp) REVERT: A 49 ARG cc_start: 0.8334 (ttt-90) cc_final: 0.7248 (mtm-85) REVERT: A 81 ARG cc_start: 0.8273 (ttp80) cc_final: 0.8065 (ttp-110) REVERT: A 82 GLU cc_start: 0.8447 (mm-30) cc_final: 0.8110 (mm-30) REVERT: A 92 ARG cc_start: 0.8370 (mtt90) cc_final: 0.7163 (ttp80) REVERT: A 250 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7138 (mtm110) REVERT: A 252 GLU cc_start: 0.9191 (tt0) cc_final: 0.8916 (tt0) REVERT: A 326 GLN cc_start: 0.8869 (mp-120) cc_final: 0.8645 (mp10) REVERT: A 329 MET cc_start: 0.7948 (mtt) cc_final: 0.7590 (mtp) REVERT: B 81 MET cc_start: 0.4522 (tpt) cc_final: 0.4188 (ttp) REVERT: C 15 LEU cc_start: 0.6098 (tp) cc_final: 0.5490 (pp) REVERT: C 66 ARG cc_start: 0.5074 (OUTLIER) cc_final: 0.4568 (ptm160) outliers start: 17 outliers final: 6 residues processed: 71 average time/residue: 0.0790 time to fit residues: 7.1881 Evaluate side-chains 63 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 266 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 66 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.0270 chunk 10 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 35 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.184512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.110180 restraints weight = 5359.260| |-----------------------------------------------------------------------------| r_work (start): 0.3132 rms_B_bonded: 2.58 r_work: 0.2984 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4738 Z= 0.117 Angle : 0.542 9.196 6445 Z= 0.274 Chirality : 0.040 0.142 761 Planarity : 0.003 0.032 793 Dihedral : 4.699 52.577 653 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.83 % Allowed : 13.03 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.34), residues: 605 helix: 1.93 (0.31), residues: 285 sheet: 0.67 (0.43), residues: 131 loop : -0.44 (0.43), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 250 TYR 0.009 0.001 TYR C 49 PHE 0.013 0.001 PHE A 72 TRP 0.009 0.001 TRP B 36 HIS 0.003 0.001 HIS A 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 ( 4736) covalent geometry : angle 0.54199 / 0.27 ( 6441) SS BOND : bond 0.00184 / 0.09 ( 2) SS BOND : angle 0.29266 / 0.14 ( 4) hydrogen bonds : bond 0.03778 / 2.78 ( 283) hydrogen bonds : angle 5.08342 / 3.73 ( 816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.202 Fit side-chains revert: symmetry clash REVERT: A 5 HIS cc_start: 0.7378 (OUTLIER) cc_final: 0.6942 (t-170) REVERT: A 49 ARG cc_start: 0.8396 (ttt-90) cc_final: 0.7078 (mtm-85) REVERT: A 81 ARG cc_start: 0.8420 (ttp80) cc_final: 0.8171 (ttp-110) REVERT: A 82 GLU cc_start: 0.8412 (mm-30) cc_final: 0.8177 (mm-30) REVERT: A 84 MET cc_start: 0.8416 (mtp) cc_final: 0.8079 (mmt) REVERT: A 92 ARG cc_start: 0.8390 (mtt90) cc_final: 0.7243 (ttp80) REVERT: A 93 GLN cc_start: 0.8598 (mt0) cc_final: 0.8366 (mt0) REVERT: A 250 ARG cc_start: 0.7994 (mtt90) cc_final: 0.7175 (mtm110) REVERT: A 326 GLN cc_start: 0.8878 (mp-120) cc_final: 0.8643 (mp10) REVERT: B 81 MET cc_start: 0.4480 (tpt) cc_final: 0.3974 (tmm) REVERT: C 15 LEU cc_start: 0.6086 (tp) cc_final: 0.5373 (pp) REVERT: C 66 ARG cc_start: 0.5384 (OUTLIER) cc_final: 0.4959 (ptm160) outliers start: 9 outliers final: 4 residues processed: 63 average time/residue: 0.0818 time to fit residues: 6.5738 Evaluate side-chains 58 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain C residue 66 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 1 optimal weight: 0.7980 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 5 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 45 optimal weight: 20.0000 chunk 49 optimal weight: 8.9990 chunk 37 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.180155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.105940 restraints weight = 5343.990| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.53 r_work: 0.2796 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4738 Z= 0.186 Angle : 0.594 8.754 6445 Z= 0.298 Chirality : 0.042 0.139 761 Planarity : 0.004 0.035 793 Dihedral : 4.904 52.419 653 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.24 % Allowed : 13.03 % Favored : 84.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.26 (0.34), residues: 605 helix: 1.71 (0.31), residues: 285 sheet: 0.76 (0.42), residues: 132 loop : -0.38 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 250 TYR 0.011 0.001 TYR C 49 PHE 0.015 0.001 PHE A 72 TRP 0.008 0.001 TRP A 37 HIS 0.005 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 ( 4736) covalent geometry : angle 0.59376 / 0.30 ( 6441) SS BOND : bond 0.00319 / 0.15 ( 2) SS BOND : angle 0.47171 / 0.22 ( 4) hydrogen bonds : bond 0.04173 / 3.03 ( 283) hydrogen bonds : angle 5.01053 / 3.67 ( 816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.168 Fit side-chains REVERT: A 5 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.7315 (t-170) REVERT: A 82 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8193 (mm-30) REVERT: A 84 MET cc_start: 0.8454 (mtp) cc_final: 0.8094 (mmt) REVERT: A 92 ARG cc_start: 0.8452 (mtt90) cc_final: 0.7322 (ttp80) REVERT: A 93 GLN cc_start: 0.8662 (mt0) cc_final: 0.8288 (mt0) REVERT: A 250 ARG cc_start: 0.8006 (mtt90) cc_final: 0.7737 (mtt-85) REVERT: A 252 GLU cc_start: 0.9010 (tt0) cc_final: 0.8807 (tt0) REVERT: A 326 GLN cc_start: 0.8853 (mp-120) cc_final: 0.8633 (mp10) REVERT: B 81 MET cc_start: 0.4651 (tpt) cc_final: 0.3997 (tmm) REVERT: B 101 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7442 (m-10) REVERT: C 15 LEU cc_start: 0.5993 (tp) cc_final: 0.5303 (pp) REVERT: C 66 ARG cc_start: 0.5596 (OUTLIER) cc_final: 0.5153 (ptm160) outliers start: 11 outliers final: 7 residues processed: 71 average time/residue: 0.0651 time to fit residues: 6.1876 Evaluate side-chains 74 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 64 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 66 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 52 optimal weight: 8.9990 chunk 31 optimal weight: 0.0000 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 50 optimal weight: 0.1980 chunk 44 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.182337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.108763 restraints weight = 5338.899| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.55 r_work: 0.2837 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2695 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.3150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4738 Z= 0.116 Angle : 0.540 9.935 6445 Z= 0.270 Chirality : 0.040 0.145 761 Planarity : 0.003 0.033 793 Dihedral : 4.710 51.372 653 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.85 % Allowed : 13.44 % Favored : 83.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.34), residues: 605 helix: 1.84 (0.31), residues: 285 sheet: 0.86 (0.43), residues: 132 loop : -0.45 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.015 0.001 TYR A 117 PHE 0.013 0.001 PHE A 72 TRP 0.009 0.001 TRP A 216 HIS 0.002 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.12 ( 4736) covalent geometry : angle 0.54057 / 0.27 ( 6441) SS BOND : bond 0.00027 / 0.01 ( 2) SS BOND : angle 0.40468 / 0.19 ( 4) hydrogen bonds : bond 0.03549 / 2.61 ( 283) hydrogen bonds : angle 4.88863 / 3.58 ( 816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.165 Fit side-chains REVERT: A 5 HIS cc_start: 0.7629 (OUTLIER) cc_final: 0.7294 (t-170) REVERT: A 82 GLU cc_start: 0.8417 (mm-30) cc_final: 0.8117 (mm-30) REVERT: A 84 MET cc_start: 0.8372 (mtp) cc_final: 0.8065 (mmt) REVERT: A 92 ARG cc_start: 0.8443 (mtt90) cc_final: 0.7295 (ttp80) REVERT: A 93 GLN cc_start: 0.8673 (mt0) cc_final: 0.8421 (mt0) REVERT: A 250 ARG cc_start: 0.7984 (mtt90) cc_final: 0.7330 (ttp80) REVERT: A 313 ARG cc_start: 0.8013 (tpt90) cc_final: 0.7437 (mmp80) REVERT: A 326 GLN cc_start: 0.8818 (mp-120) cc_final: 0.8584 (mp10) REVERT: B 81 MET cc_start: 0.4532 (tpt) cc_final: 0.4017 (tmm) REVERT: B 101 TYR cc_start: 0.7723 (OUTLIER) cc_final: 0.7359 (m-10) REVERT: C 66 ARG cc_start: 0.5720 (OUTLIER) cc_final: 0.5328 (ptm160) outliers start: 14 outliers final: 8 residues processed: 76 average time/residue: 0.0671 time to fit residues: 6.7277 Evaluate side-chains 78 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 101 TYR Chi-restraints excluded: chain C residue 66 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 18 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 46 optimal weight: 8.9990 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.183663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.109021 restraints weight = 5439.047| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.64 r_work: 0.2891 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4738 Z= 0.126 Angle : 0.539 10.324 6445 Z= 0.268 Chirality : 0.040 0.140 761 Planarity : 0.003 0.033 793 Dihedral : 4.564 49.957 653 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.44 % Allowed : 14.87 % Favored : 82.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.34), residues: 605 helix: 1.88 (0.31), residues: 285 sheet: 0.94 (0.43), residues: 132 loop : -0.44 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 250 TYR 0.017 0.001 TYR A 117 PHE 0.013 0.001 PHE A 72 TRP 0.009 0.001 TRP A 216 HIS 0.004 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 4736) covalent geometry : angle 0.53944 / 0.27 ( 6441) SS BOND : bond 0.00074 / 0.04 ( 2) SS BOND : angle 0.34611 / 0.16 ( 4) hydrogen bonds : bond 0.03529 / 2.61 ( 283) hydrogen bonds : angle 4.81503 / 3.52 ( 816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.161 Fit side-chains REVERT: A 5 HIS cc_start: 0.7612 (OUTLIER) cc_final: 0.7259 (t-170) REVERT: A 58 ASN cc_start: 0.8349 (p0) cc_final: 0.7979 (m-40) REVERT: A 82 GLU cc_start: 0.8430 (mm-30) cc_final: 0.8134 (mm-30) REVERT: A 84 MET cc_start: 0.8312 (mtp) cc_final: 0.8024 (mmt) REVERT: A 92 ARG cc_start: 0.8451 (mtt90) cc_final: 0.7462 (ttp80) REVERT: A 93 GLN cc_start: 0.8686 (mt0) cc_final: 0.8428 (mt0) REVERT: A 250 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7161 (mtm110) REVERT: A 326 GLN cc_start: 0.8835 (mp-120) cc_final: 0.8579 (mp10) REVERT: B 81 MET cc_start: 0.4721 (tpt) cc_final: 0.4053 (tmm) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.0537 time to fit residues: 5.0727 Evaluate side-chains 71 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 60 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 103 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 0.0070 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 45 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.8800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 253 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.183959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.110033 restraints weight = 5330.898| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.58 r_work: 0.2848 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2705 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4738 Z= 0.119 Angle : 0.534 11.550 6445 Z= 0.263 Chirality : 0.040 0.140 761 Planarity : 0.003 0.033 793 Dihedral : 4.481 49.119 653 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 3.05 % Allowed : 15.48 % Favored : 81.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.34), residues: 605 helix: 1.93 (0.31), residues: 285 sheet: 1.08 (0.44), residues: 132 loop : -0.46 (0.45), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.018 0.001 TYR A 117 PHE 0.013 0.001 PHE A 72 TRP 0.010 0.001 TRP A 216 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 4736) covalent geometry : angle 0.53396 / 0.26 ( 6441) SS BOND : bond 0.00161 / 0.08 ( 2) SS BOND : angle 0.18168 / 0.09 ( 4) hydrogen bonds : bond 0.03424 / 2.53 ( 283) hydrogen bonds : angle 4.77935 / 3.50 ( 816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 0.169 Fit side-chains REVERT: A 5 HIS cc_start: 0.7637 (OUTLIER) cc_final: 0.7313 (t-170) REVERT: A 58 ASN cc_start: 0.8263 (p0) cc_final: 0.7997 (m-40) REVERT: A 82 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8081 (mm-30) REVERT: A 84 MET cc_start: 0.8281 (mtp) cc_final: 0.7984 (mmt) REVERT: A 92 ARG cc_start: 0.8463 (mtt90) cc_final: 0.7486 (ttp80) REVERT: A 93 GLN cc_start: 0.8674 (mt0) cc_final: 0.8408 (mt0) REVERT: A 250 ARG cc_start: 0.8015 (mtt90) cc_final: 0.7125 (mtm110) REVERT: A 326 GLN cc_start: 0.8804 (mp-120) cc_final: 0.8557 (mp10) REVERT: B 81 MET cc_start: 0.4714 (tpt) cc_final: 0.4069 (tmm) REVERT: C 66 ARG cc_start: 0.5780 (OUTLIER) cc_final: 0.5517 (ptm160) outliers start: 15 outliers final: 10 residues processed: 73 average time/residue: 0.0674 time to fit residues: 6.5763 Evaluate side-chains 72 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 78 THR Chi-restraints excluded: chain B residue 99 GLU Chi-restraints excluded: chain B residue 103 ASN Chi-restraints excluded: chain C residue 66 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 19 optimal weight: 0.8980 chunk 47 optimal weight: 30.0000 chunk 11 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.184984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.111524 restraints weight = 5400.624| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.59 r_work: 0.2867 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 4738 Z= 0.105 Angle : 0.526 11.870 6445 Z= 0.260 Chirality : 0.039 0.139 761 Planarity : 0.003 0.032 793 Dihedral : 4.371 48.133 653 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.04 % Allowed : 17.72 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.54 (0.34), residues: 605 helix: 1.92 (0.31), residues: 287 sheet: 1.16 (0.44), residues: 132 loop : -0.48 (0.45), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.018 0.001 TYR A 117 PHE 0.012 0.001 PHE A 72 TRP 0.011 0.001 TRP A 216 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.11 ( 4736) covalent geometry : angle 0.52621 / 0.26 ( 6441) SS BOND : bond 0.00107 / 0.05 ( 2) SS BOND : angle 0.21163 / 0.09 ( 4) hydrogen bonds : bond 0.03269 / 2.44 ( 283) hydrogen bonds : angle 4.76164 / 3.48 ( 816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.165 Fit side-chains revert: symmetry clash REVERT: A 5 HIS cc_start: 0.7646 (OUTLIER) cc_final: 0.7309 (t-170) REVERT: A 82 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8051 (mm-30) REVERT: A 84 MET cc_start: 0.8277 (mtp) cc_final: 0.8019 (mmt) REVERT: A 92 ARG cc_start: 0.8474 (mtt90) cc_final: 0.7514 (ttp80) REVERT: A 250 ARG cc_start: 0.8001 (mtt90) cc_final: 0.7102 (mtm110) REVERT: A 313 ARG cc_start: 0.8016 (tpt90) cc_final: 0.7472 (mmp80) REVERT: A 326 GLN cc_start: 0.8805 (mp-120) cc_final: 0.8548 (mp10) REVERT: B 81 MET cc_start: 0.4602 (tpt) cc_final: 0.4091 (tmm) REVERT: C 65 SER cc_start: 0.7658 (t) cc_final: 0.7149 (p) outliers start: 10 outliers final: 7 residues processed: 74 average time/residue: 0.0646 time to fit residues: 6.3421 Evaluate side-chains 71 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 5 optimal weight: 5.9990 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 43 optimal weight: 0.0170 chunk 9 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 17 optimal weight: 0.0470 chunk 19 optimal weight: 1.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 58 ASN A 116 ASN A 253 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.184343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.111361 restraints weight = 5315.318| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.50 r_work: 0.2888 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.3727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4738 Z= 0.112 Angle : 0.533 11.994 6445 Z= 0.262 Chirality : 0.039 0.140 761 Planarity : 0.003 0.032 793 Dihedral : 4.317 46.174 653 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.83 % Allowed : 17.52 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.49 (0.35), residues: 605 helix: 1.94 (0.31), residues: 288 sheet: 1.20 (0.47), residues: 122 loop : -0.59 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.018 0.001 TYR A 117 PHE 0.012 0.001 PHE A 72 TRP 0.011 0.001 TRP A 309 HIS 0.003 0.001 HIS A 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.11 ( 4736) covalent geometry : angle 0.53285 / 0.26 ( 6441) SS BOND : bond 0.00142 / 0.07 ( 2) SS BOND : angle 0.15409 / 0.07 ( 4) hydrogen bonds : bond 0.03335 / 2.48 ( 283) hydrogen bonds : angle 4.75793 / 3.48 ( 816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.177 Fit side-chains revert: symmetry clash REVERT: A 5 HIS cc_start: 0.7574 (OUTLIER) cc_final: 0.7180 (t-170) REVERT: A 26 MET cc_start: 0.9046 (mmm) cc_final: 0.8846 (mmm) REVERT: A 82 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8043 (mm-30) REVERT: A 84 MET cc_start: 0.8296 (mtp) cc_final: 0.8027 (mmt) REVERT: A 92 ARG cc_start: 0.8481 (mtt90) cc_final: 0.7544 (ttp80) REVERT: A 250 ARG cc_start: 0.7990 (mtt90) cc_final: 0.7088 (mtm110) REVERT: A 313 ARG cc_start: 0.8027 (tpt90) cc_final: 0.7480 (mmp80) REVERT: A 326 GLN cc_start: 0.8817 (mp-120) cc_final: 0.8532 (mp10) REVERT: A 329 MET cc_start: 0.7995 (mtt) cc_final: 0.7648 (mtp) REVERT: B 81 MET cc_start: 0.4598 (tpt) cc_final: 0.4053 (tmm) REVERT: C 65 SER cc_start: 0.7717 (t) cc_final: 0.7202 (p) outliers start: 9 outliers final: 7 residues processed: 72 average time/residue: 0.0769 time to fit residues: 7.1665 Evaluate side-chains 73 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 34 THR Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 8 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.4980 chunk 42 optimal weight: 0.0020 chunk 41 optimal weight: 5.9990 chunk 14 optimal weight: 0.2980 chunk 54 optimal weight: 9.9990 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 6.9990 chunk 45 optimal weight: 10.0000 overall best weight: 0.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.186156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.113981 restraints weight = 5314.202| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.53 r_work: 0.3032 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4738 Z= 0.097 Angle : 0.520 12.270 6445 Z= 0.256 Chirality : 0.039 0.139 761 Planarity : 0.003 0.032 793 Dihedral : 4.167 44.158 653 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.43 % Allowed : 19.14 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.35), residues: 605 helix: 2.02 (0.31), residues: 288 sheet: 1.42 (0.49), residues: 114 loop : -0.68 (0.42), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 250 TYR 0.020 0.001 TYR A 117 PHE 0.010 0.001 PHE A 72 TRP 0.013 0.001 TRP A 216 HIS 0.003 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00217 / 0.10 ( 4736) covalent geometry : angle 0.52011 / 0.26 ( 6441) SS BOND : bond 0.00121 / 0.06 ( 2) SS BOND : angle 0.21554 / 0.10 ( 4) hydrogen bonds : bond 0.03096 / 2.33 ( 283) hydrogen bonds : angle 4.70667 / 3.43 ( 816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1210 Ramachandran restraints generated. 605 Oldfield, 0 Emsley, 605 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: A 5 HIS cc_start: 0.7469 (OUTLIER) cc_final: 0.7169 (t-170) REVERT: A 82 GLU cc_start: 0.8422 (mm-30) cc_final: 0.8101 (mm-30) REVERT: A 92 ARG cc_start: 0.8510 (mtt90) cc_final: 0.7619 (ttp80) REVERT: A 250 ARG cc_start: 0.8055 (mtt90) cc_final: 0.7185 (mtm110) REVERT: A 313 ARG cc_start: 0.8010 (tpt90) cc_final: 0.7512 (mmp80) REVERT: A 329 MET cc_start: 0.7965 (mtt) cc_final: 0.7574 (mtp) REVERT: B 33 GLU cc_start: 0.7472 (pt0) cc_final: 0.7001 (pm20) REVERT: B 81 MET cc_start: 0.4656 (tpt) cc_final: 0.4093 (tmm) REVERT: C 65 SER cc_start: 0.7801 (t) cc_final: 0.7133 (p) REVERT: C 66 ARG cc_start: 0.5868 (ppp80) cc_final: 0.5591 (ptm160) outliers start: 7 outliers final: 5 residues processed: 73 average time/residue: 0.0785 time to fit residues: 7.3441 Evaluate side-chains 71 residues out of total 491 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 65 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 HIS Chi-restraints excluded: chain A residue 240 LYS Chi-restraints excluded: chain A residue 305 SER Chi-restraints excluded: chain A residue 308 CYS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 71 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 14 optimal weight: 0.4980 chunk 30 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 52 optimal weight: 9.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 15 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 0.0270 chunk 49 optimal weight: 0.3980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.186577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.114283 restraints weight = 5385.930| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 2.56 r_work: 0.3000 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2853 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.3947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4738 Z= 0.100 Angle : 0.536 14.345 6445 Z= 0.261 Chirality : 0.039 0.139 761 Planarity : 0.003 0.031 793 Dihedral : 4.190 45.138 653 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.43 % Allowed : 19.35 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.35), residues: 605 helix: 2.08 (0.31), residues: 288 sheet: 1.51 (0.50), residues: 114 loop : -0.67 (0.43), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.018 0.001 TYR A 117 PHE 0.010 0.001 PHE A 72 TRP 0.012 0.001 TRP A 309 HIS 0.003 0.001 HIS A 3 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.10 ( 4736) covalent geometry : angle 0.53658 / 0.26 ( 6441) SS BOND : bond 0.00143 / 0.07 ( 2) SS BOND : angle 0.17079 / 0.08 ( 4) hydrogen bonds : bond 0.03085 / 2.32 ( 283) hydrogen bonds : angle 4.66502 / 3.41 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.89 seconds wall clock time: 28 minutes 39.28 seconds (1719.28 seconds total)