Starting phenix.real_space_refine on Tue Aug 4 16:04:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rh8_53961/08_2026/9rh8_53961.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rh8_53961/08_2026/9rh8_53961.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9rh8_53961/08_2026/9rh8_53961.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rh8_53961/08_2026/9rh8_53961.map" model { file = "/net/cci-nas-00/data/ceres_data/9rh8_53961/08_2026/9rh8_53961.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rh8_53961/08_2026/9rh8_53961.cif" } 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 3013 2.51 5 N 755 2.21 5 O 836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s 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: 4623 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 2900 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 15, 'TRANS': 370} 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: 1.29, per 1000 atoms: 0.28 Number of scatterers: 4623 At special positions: 0 Unit cell: (67.797, 76.167, 102.951, 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 836 8.00 N 755 7.00 C 3013 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: 0.37 Conformation dependent library (CDL) restraints added in 179.9 milliseconds 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1108 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 6 sheets defined 53.1% alpha, 18.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'A' and resid 3 through 10 Processing helix chain 'A' and resid 12 through 31 removed outlier: 3.692A pdb=" N LEU A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 43 removed outlier: 4.796A pdb=" N GLY A 36 " --> pdb=" O GLY A 32 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N TRP A 37 " --> pdb=" O ALA A 33 " (cutoff:3.500A) Processing helix chain 'A' and resid 59 through 86 removed outlier: 3.532A pdb=" N VAL A 70 " --> pdb=" O ALA A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 90 removed outlier: 4.337A pdb=" N SER A 90 " --> pdb=" O SER A 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 87 through 90' Processing helix chain 'A' and resid 94 through 117 removed outlier: 3.621A pdb=" N VAL A 107 " --> pdb=" O GLY A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix removed outlier: 3.631A pdb=" N PHE A 115 " --> pdb=" O LEU A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 128 removed outlier: 3.512A pdb=" N TRP A 126 " --> pdb=" O ARG A 123 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N ALA A 127 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 144 removed outlier: 3.727A pdb=" N LEU A 144 " --> pdb=" O VAL A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 148 removed outlier: 3.702A pdb=" N VAL A 148 " --> pdb=" O GLY A 145 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 145 through 148' Processing helix chain 'A' and resid 149 through 175 Processing helix chain 'A' and resid 180 through 200 Processing helix chain 'A' and resid 204 through 219 removed outlier: 3.712A pdb=" N TYR A 208 " --> pdb=" O ARG A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 237 removed outlier: 3.997A pdb=" N GLY A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.652A 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 Processing helix chain 'A' and resid 338 through 351 Processing helix chain 'A' and resid 354 through 384 removed outlier: 3.760A pdb=" N VAL A 382 " --> pdb=" O SER A 378 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 83 removed outlier: 3.689A pdb=" N PHE C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) 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: 3.794A pdb=" N LYS B 3 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU B 25 " --> pdb=" O LYS B 3 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12 removed outlier: 6.601A pdb=" N MET B 34 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ALA B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 7.069A 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: 7.068A pdb=" N CYS B 96 " --> pdb=" O TRP B 108 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N TRP B 108 " --> pdb=" O CYS B 96 " (cutoff:3.500A) removed outlier: 7.076A 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 6 Processing sheet with id=AA6, first strand: chain 'C' and resid 10 through 12 removed outlier: 3.511A pdb=" N ALA C 84 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 5.071A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) 293 hydrogen bonds defined for protein. 828 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: 0.45 Time building geometry restraints manager: 0.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1442 1.35 - 1.46: 1132 1.46 - 1.58: 2122 1.58 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 4727 Sorted by residual: bond pdb=" N SER A 10 " pdb=" CA SER A 10 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.32e-02 5.74e+03 6.95e+00 bond pdb=" N PHE A 7 " pdb=" CA PHE A 7 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.17e-02 7.31e+03 6.67e+00 bond pdb=" N PHE A 8 " pdb=" CA PHE A 8 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.35e-02 5.49e+03 6.53e+00 bond pdb=" N SER A 9 " pdb=" CA SER A 9 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.18e-02 7.18e+03 6.00e+00 bond pdb=" N LEU A 4 " pdb=" CA LEU A 4 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.27e-02 6.20e+03 4.73e+00 ... (remaining 4722 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 6169 1.22 - 2.44: 201 2.44 - 3.66: 38 3.66 - 4.88: 17 4.88 - 6.10: 5 Bond angle restraints: 6430 Sorted by residual: angle pdb=" N ILE C 29 " pdb=" CA ILE C 29 " pdb=" C ILE C 29 " ideal model delta sigma weight residual 113.47 109.50 3.97 1.01e+00 9.80e-01 1.54e+01 angle pdb=" CA SER A 10 " pdb=" C SER A 10 " pdb=" O SER A 10 " ideal model delta sigma weight residual 121.87 118.39 3.48 1.10e+00 8.26e-01 1.00e+01 angle pdb=" CA TRP A 309 " pdb=" CB TRP A 309 " pdb=" CG TRP A 309 " ideal model delta sigma weight residual 113.60 119.22 -5.62 1.90e+00 2.77e-01 8.75e+00 angle pdb=" N LEU A 4 " pdb=" CA LEU A 4 " pdb=" C LEU A 4 " ideal model delta sigma weight residual 111.75 107.97 3.78 1.28e+00 6.10e-01 8.70e+00 angle pdb=" N PHE A 8 " pdb=" CA PHE A 8 " pdb=" C PHE A 8 " ideal model delta sigma weight residual 113.01 109.48 3.53 1.20e+00 6.94e-01 8.64e+00 ... (remaining 6425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 2506 16.88 - 33.75: 191 33.75 - 50.62: 55 50.62 - 67.50: 9 67.50 - 84.37: 4 Dihedral angle restraints: 2765 sinusoidal: 1027 harmonic: 1738 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 96 " pdb=" CB CYS B 96 " ideal model delta sinusoidal sigma weight residual 93.00 51.82 41.18 1 1.00e+01 1.00e-02 2.37e+01 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 53.69 39.31 1 1.00e+01 1.00e-02 2.17e+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 180.00 162.49 17.51 0 5.00e+00 4.00e-02 1.23e+01 ... (remaining 2762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 510 0.033 - 0.065: 177 0.065 - 0.098: 44 0.098 - 0.131: 27 0.131 - 0.164: 2 Chirality restraints: 760 Sorted by residual: chirality pdb=" CA THR C 7 " pdb=" N THR C 7 " pdb=" C THR C 7 " pdb=" CB THR C 7 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.16 2.00e-01 2.50e+01 6.69e-01 chirality pdb=" CA HIS A 256 " pdb=" N HIS A 256 " pdb=" C HIS A 256 " pdb=" CB HIS A 256 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.33e-01 chirality pdb=" CA LYS A 315 " pdb=" N LYS A 315 " pdb=" C LYS A 315 " pdb=" CB LYS A 315 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 757 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 117 " 0.008 2.00e-02 2.50e+03 1.03e-02 2.12e+00 pdb=" CG TYR A 117 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 117 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 117 " 0.009 2.00e-02 2.50e+03 pdb=" CE1 TYR A 117 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 117 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 117 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 117 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 58 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO C 59 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO C 59 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 59 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 264 " -0.015 5.00e-02 4.00e+02 2.21e-02 7.80e-01 pdb=" N PRO A 265 " 0.038 5.00e-02 4.00e+02 pdb=" CA PRO A 265 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO A 265 " -0.013 5.00e-02 4.00e+02 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 901 2.77 - 3.31: 4399 3.31 - 3.84: 7580 3.84 - 4.37: 8949 4.37 - 4.90: 15750 Nonbonded interactions: 37579 Sorted by model distance: nonbonded pdb=" NE2 GLN A 47 " pdb=" OE2 GLU A 54 " model vdw 2.243 3.120 nonbonded pdb=" OD1 ASP A 133 " pdb=" OG1 THR A 340 " model vdw 2.272 3.040 nonbonded pdb=" OH TYR A 38 " pdb=" O PHE A 269 " model vdw 2.285 3.040 nonbonded pdb=" OG SER C 34 " pdb=" O ILE C 48 " model vdw 2.322 3.040 nonbonded pdb=" O PRO C 8 " pdb=" OG1 THR C 102 " model vdw 2.343 3.040 ... (remaining 37574 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 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: 0.010 Process input model: 5.920 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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:0.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.003 0.036 4729 Z= 0.177 Angle : 0.570 6.101 6434 Z= 0.332 Chirality : 0.039 0.164 760 Planarity : 0.003 0.033 792 Dihedral : 13.490 84.373 1651 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.00 % Allowed : 8.98 % Favored : 91.02 % 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: 0.76 (0.34), residues: 604 helix: 0.65 (0.29), residues: 292 sheet: 0.90 (0.51), residues: 107 loop : 0.31 (0.46), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 92 TYR 0.025 0.001 TYR A 117 PHE 0.008 0.001 PHE A 72 TRP 0.010 0.001 TRP C 35 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.18 ( 4727) covalent geometry : angle 0.56997 / 0.33 ( 6430) SS BOND : bond 0.00190 / 0.09 ( 2) SS BOND : angle 0.37212 / 0.23 ( 4) hydrogen bonds : bond 0.21930 / 15.03 ( 286) hydrogen bonds : angle 8.18603 / 6.00 ( 828) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.101 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.0537 time to fit residues: 3.9858 Evaluate side-chains 54 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 0.0770 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 58 optimal weight: 9.9990 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 58 ASN A 116 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.185545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112179 restraints weight = 5437.813| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.60 r_work: 0.3080 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4729 Z= 0.123 Angle : 0.543 6.075 6434 Z= 0.286 Chirality : 0.039 0.161 760 Planarity : 0.004 0.031 792 Dihedral : 3.941 17.189 650 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.43 % Allowed : 8.98 % Favored : 89.59 % 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: 1.25 (0.34), residues: 604 helix: 1.30 (0.29), residues: 297 sheet: 0.64 (0.50), residues: 107 loop : 0.43 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 92 TYR 0.011 0.001 TYR A 38 PHE 0.008 0.001 PHE A 72 TRP 0.009 0.001 TRP A 62 HIS 0.001 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 ( 4727) covalent geometry : angle 0.54323 / 0.29 ( 6430) SS BOND : bond 0.00317 / 0.15 ( 2) SS BOND : angle 0.55270 / 0.42 ( 4) hydrogen bonds : bond 0.04416 / 2.98 ( 286) hydrogen bonds : angle 5.52367 / 4.06 ( 828) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.168 Fit side-chains REVERT: A 43 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7789 (mt-10) REVERT: A 47 GLN cc_start: 0.8280 (tt0) cc_final: 0.8031 (tp40) REVERT: A 68 MET cc_start: 0.9197 (mmm) cc_final: 0.8889 (mmp) REVERT: A 298 ILE cc_start: 0.8714 (mm) cc_final: 0.8478 (mt) outliers start: 7 outliers final: 7 residues processed: 60 average time/residue: 0.0698 time to fit residues: 5.4738 Evaluate side-chains 61 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 315 LYS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 48 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 chunk 55 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 0.0040 chunk 42 optimal weight: 0.0050 chunk 41 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 overall best weight: 0.9610 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.186561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.111955 restraints weight = 5425.508| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.58 r_work: 0.3059 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4729 Z= 0.120 Angle : 0.521 6.416 6434 Z= 0.269 Chirality : 0.039 0.159 760 Planarity : 0.003 0.030 792 Dihedral : 3.881 17.351 650 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.24 % Allowed : 10.41 % Favored : 87.35 % 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: 1.40 (0.34), residues: 604 helix: 1.51 (0.29), residues: 297 sheet: 0.59 (0.51), residues: 107 loop : 0.42 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 92 TYR 0.009 0.001 TYR C 49 PHE 0.009 0.001 PHE A 71 TRP 0.009 0.001 TRP A 216 HIS 0.001 0.000 HIS B 52 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 ( 4727) covalent geometry : angle 0.52138 / 0.27 ( 6430) SS BOND : bond 0.00335 / 0.16 ( 2) SS BOND : angle 0.61856 / 0.49 ( 4) hydrogen bonds : bond 0.03651 / 2.47 ( 286) hydrogen bonds : angle 5.12061 / 3.76 ( 828) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.169 Fit side-chains REVERT: A 43 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7755 (mt-10) REVERT: A 56 ASN cc_start: 0.8561 (m-40) cc_final: 0.8218 (m-40) REVERT: A 256 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7397 (m-70) outliers start: 11 outliers final: 8 residues processed: 64 average time/residue: 0.0635 time to fit residues: 5.4172 Evaluate side-chains 63 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 54 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.7980 chunk 52 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 20.0000 chunk 17 optimal weight: 0.4980 chunk 47 optimal weight: 6.9990 chunk 15 optimal weight: 0.7980 chunk 42 optimal weight: 0.3980 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4096 r_free = 0.4096 target = 0.186947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.112914 restraints weight = 5395.219| |-----------------------------------------------------------------------------| r_work (start): 0.3092 rms_B_bonded: 2.62 r_work: 0.2959 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4729 Z= 0.102 Angle : 0.494 6.406 6434 Z= 0.256 Chirality : 0.038 0.157 760 Planarity : 0.003 0.029 792 Dihedral : 3.764 16.965 650 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 1.63 % Allowed : 10.82 % Favored : 87.55 % 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: 1.60 (0.35), residues: 604 helix: 1.75 (0.29), residues: 297 sheet: 0.65 (0.51), residues: 107 loop : 0.41 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 92 TYR 0.010 0.001 TYR A 38 PHE 0.007 0.001 PHE A 71 TRP 0.009 0.001 TRP A 216 HIS 0.001 0.000 HIS B 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 ( 4727) covalent geometry : angle 0.49423 / 0.26 ( 6430) SS BOND : bond 0.00309 / 0.15 ( 2) SS BOND : angle 0.52794 / 0.43 ( 4) hydrogen bonds : bond 0.03174 / 2.19 ( 286) hydrogen bonds : angle 4.85961 / 3.56 ( 828) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 62 time to evaluate : 0.166 Fit side-chains REVERT: A 56 ASN cc_start: 0.8192 (m-40) cc_final: 0.7867 (m-40) REVERT: A 256 HIS cc_start: 0.7996 (OUTLIER) cc_final: 0.7233 (m-70) outliers start: 8 outliers final: 5 residues processed: 66 average time/residue: 0.0693 time to fit residues: 6.0277 Evaluate side-chains 66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 52 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 11 optimal weight: 0.8980 chunk 49 optimal weight: 0.0670 chunk 8 optimal weight: 4.9990 chunk 42 optimal weight: 20.0000 chunk 46 optimal weight: 30.0000 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 overall best weight: 0.9922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.185752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.111067 restraints weight = 5418.897| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.64 r_work: 0.2936 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2798 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4729 Z= 0.118 Angle : 0.504 6.445 6434 Z= 0.260 Chirality : 0.038 0.157 760 Planarity : 0.003 0.029 792 Dihedral : 3.787 17.142 650 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.45 % Allowed : 10.61 % Favored : 86.94 % 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: 1.62 (0.35), residues: 604 helix: 1.76 (0.29), residues: 297 sheet: 0.71 (0.51), residues: 107 loop : 0.37 (0.47), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.010 0.001 TYR C 49 PHE 0.009 0.001 PHE A 72 TRP 0.008 0.001 TRP A 216 HIS 0.001 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.12 ( 4727) covalent geometry : angle 0.50368 / 0.26 ( 6430) SS BOND : bond 0.00333 / 0.16 ( 2) SS BOND : angle 0.62431 / 0.53 ( 4) hydrogen bonds : bond 0.03290 / 2.27 ( 286) hydrogen bonds : angle 4.82209 / 3.54 ( 828) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.099 Fit side-chains REVERT: A 256 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7178 (m-70) outliers start: 12 outliers final: 10 residues processed: 69 average time/residue: 0.0634 time to fit residues: 5.7764 Evaluate side-chains 72 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 54 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 16 optimal weight: 0.7980 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 20.0000 chunk 20 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN A 116 ASN A 177 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.185839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111311 restraints weight = 5527.812| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 2.66 r_work: 0.3069 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2928 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4729 Z= 0.125 Angle : 0.503 5.434 6434 Z= 0.259 Chirality : 0.039 0.159 760 Planarity : 0.003 0.029 792 Dihedral : 3.804 17.040 650 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 2.65 % Allowed : 11.43 % Favored : 85.92 % 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: 1.59 (0.35), residues: 604 helix: 1.74 (0.30), residues: 297 sheet: 0.75 (0.50), residues: 108 loop : 0.32 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.011 0.001 TYR A 38 PHE 0.009 0.001 PHE A 72 TRP 0.008 0.001 TRP A 216 HIS 0.001 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 4727) covalent geometry : angle 0.50297 / 0.26 ( 6430) SS BOND : bond 0.00292 / 0.14 ( 2) SS BOND : angle 0.54859 / 0.46 ( 4) hydrogen bonds : bond 0.03243 / 2.21 ( 286) hydrogen bonds : angle 4.80424 / 3.52 ( 828) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 59 time to evaluate : 0.098 Fit side-chains REVERT: A 256 HIS cc_start: 0.8198 (OUTLIER) cc_final: 0.7395 (m-70) outliers start: 13 outliers final: 11 residues processed: 66 average time/residue: 0.0539 time to fit residues: 4.7732 Evaluate side-chains 68 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 54 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 54 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 21 optimal weight: 2.9990 chunk 46 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 30 ASN A 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.186535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111280 restraints weight = 5421.027| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.62 r_work: 0.3009 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4729 Z= 0.130 Angle : 0.507 5.453 6434 Z= 0.262 Chirality : 0.039 0.157 760 Planarity : 0.003 0.028 792 Dihedral : 3.818 17.031 650 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 3.27 % Allowed : 10.82 % Favored : 85.92 % 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: 1.57 (0.35), residues: 604 helix: 1.71 (0.30), residues: 297 sheet: 0.79 (0.50), residues: 108 loop : 0.30 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.011 0.001 TYR C 49 PHE 0.010 0.001 PHE A 72 TRP 0.009 0.001 TRP A 216 HIS 0.001 0.000 HIS B 5 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 ( 4727) covalent geometry : angle 0.50689 / 0.26 ( 6430) SS BOND : bond 0.00295 / 0.14 ( 2) SS BOND : angle 0.57304 / 0.49 ( 4) hydrogen bonds : bond 0.03253 / 2.23 ( 286) hydrogen bonds : angle 4.79856 / 3.51 ( 828) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.166 Fit side-chains REVERT: A 256 HIS cc_start: 0.8185 (OUTLIER) cc_final: 0.7378 (m-70) outliers start: 16 outliers final: 14 residues processed: 63 average time/residue: 0.0515 time to fit residues: 4.3676 Evaluate side-chains 68 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 53 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain B residue 51 ILE Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 54 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 21 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 0.6980 chunk 40 optimal weight: 30.0000 chunk 18 optimal weight: 0.9980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.184087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.109221 restraints weight = 5436.366| |-----------------------------------------------------------------------------| r_work (start): 0.3040 rms_B_bonded: 2.62 r_work: 0.2906 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4729 Z= 0.161 Angle : 0.528 5.505 6434 Z= 0.271 Chirality : 0.039 0.126 760 Planarity : 0.003 0.029 792 Dihedral : 3.909 17.200 650 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 2.86 % Allowed : 11.22 % Favored : 85.92 % 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: 1.48 (0.35), residues: 604 helix: 1.60 (0.30), residues: 297 sheet: 0.84 (0.50), residues: 108 loop : 0.28 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.012 0.001 TYR C 49 PHE 0.012 0.001 PHE A 72 TRP 0.009 0.001 TRP A 258 HIS 0.001 0.000 HIS A 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 4727) covalent geometry : angle 0.52758 / 0.27 ( 6430) SS BOND : bond 0.00303 / 0.14 ( 2) SS BOND : angle 0.60014 / 0.53 ( 4) hydrogen bonds : bond 0.03434 / 2.33 ( 286) hydrogen bonds : angle 4.85557 / 3.55 ( 828) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 52 time to evaluate : 0.168 Fit side-chains REVERT: A 256 HIS cc_start: 0.8041 (OUTLIER) cc_final: 0.7200 (m-70) outliers start: 14 outliers final: 11 residues processed: 61 average time/residue: 0.0460 time to fit residues: 3.8690 Evaluate side-chains 63 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 54 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 22 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 49 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 56 ASN A 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.186581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112640 restraints weight = 5374.194| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.59 r_work: 0.2947 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4729 Z= 0.101 Angle : 0.481 5.466 6434 Z= 0.249 Chirality : 0.038 0.129 760 Planarity : 0.003 0.028 792 Dihedral : 3.770 16.669 650 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.45 % Allowed : 11.84 % Favored : 85.71 % 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: 1.69 (0.35), residues: 604 helix: 1.77 (0.30), residues: 297 sheet: 0.97 (0.50), residues: 108 loop : 0.34 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 313 TYR 0.010 0.001 TYR A 38 PHE 0.007 0.001 PHE A 71 TRP 0.011 0.001 TRP A 216 HIS 0.001 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 ( 4727) covalent geometry : angle 0.48126 / 0.25 ( 6430) SS BOND : bond 0.00253 / 0.12 ( 2) SS BOND : angle 0.49410 / 0.40 ( 4) hydrogen bonds : bond 0.03017 / 2.08 ( 286) hydrogen bonds : angle 4.72272 / 3.46 ( 828) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.146 Fit side-chains REVERT: A 43 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7753 (mt-10) REVERT: A 256 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7253 (m-70) REVERT: A 313 ARG cc_start: 0.7698 (mmp80) cc_final: 0.7492 (mmp80) outliers start: 12 outliers final: 11 residues processed: 64 average time/residue: 0.0479 time to fit residues: 4.2051 Evaluate side-chains 67 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 ASN Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 177 ASN Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 33 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 56 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 116 ASN A 177 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.186203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.112509 restraints weight = 5433.267| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.59 r_work: 0.2954 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 4729 Z= 0.198 Angle : 1.136 59.196 6434 Z= 0.690 Chirality : 0.044 0.465 760 Planarity : 0.007 0.156 792 Dihedral : 3.947 26.143 650 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.24 % Allowed : 11.84 % Favored : 85.92 % Cbeta Deviations : 0.18 % 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: 1.72 (0.35), residues: 604 helix: 1.78 (0.30), residues: 297 sheet: 0.98 (0.50), residues: 108 loop : 0.40 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.010 0.001 TYR A 38 PHE 0.007 0.001 PHE A 72 TRP 0.010 0.001 TRP A 216 HIS 0.001 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.20 ( 4727) covalent geometry : angle 1.13598 / 0.69 ( 6430) SS BOND : bond 0.00250 / 0.12 ( 2) SS BOND : angle 0.49450 / 0.40 ( 4) hydrogen bonds : bond 0.03003 / 2.05 ( 286) hydrogen bonds : angle 4.73490 / 3.46 ( 828) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1208 Ramachandran restraints generated. 604 Oldfield, 0 Emsley, 604 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.159 Fit side-chains REVERT: A 43 GLU cc_start: 0.8062 (mt-10) cc_final: 0.7767 (mt-10) REVERT: A 256 HIS cc_start: 0.8094 (OUTLIER) cc_final: 0.7271 (m-70) REVERT: A 313 ARG cc_start: 0.7693 (mmp80) cc_final: 0.7480 (mmp80) outliers start: 11 outliers final: 9 residues processed: 61 average time/residue: 0.0457 time to fit residues: 3.8691 Evaluate side-chains 63 residues out of total 490 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 53 time to evaluate : 0.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 111 LEU Chi-restraints excluded: chain A residue 124 GLU Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 256 HIS Chi-restraints excluded: chain A residue 331 VAL Chi-restraints excluded: chain C residue 10 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 47 LEU Chi-restraints excluded: chain C residue 52 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 44 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 40 optimal weight: 40.0000 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 55 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 177 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 = 0.4087 r_free = 0.4087 target = 0.186273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.112266 restraints weight = 5443.898| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 2.60 r_work: 0.2969 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.088 4729 Z= 0.198 Angle : 1.136 59.196 6434 Z= 0.690 Chirality : 0.044 0.465 760 Planarity : 0.007 0.156 792 Dihedral : 3.947 26.143 650 Min Nonbonded Distance : 1.605 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.04 % Allowed : 12.04 % Favored : 85.92 % Cbeta Deviations : 0.18 % 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: 1.72 (0.35), residues: 604 helix: 1.78 (0.30), residues: 297 sheet: 0.98 (0.50), residues: 108 loop : 0.40 (0.47), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 313 TYR 0.010 0.001 TYR A 38 PHE 0.007 0.001 PHE A 72 TRP 0.010 0.001 TRP A 216 HIS 0.001 0.000 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.20 ( 4727) covalent geometry : angle 1.13598 / 0.69 ( 6430) SS BOND : bond 0.00250 / 0.12 ( 2) SS BOND : angle 0.49450 / 0.40 ( 4) hydrogen bonds : bond 0.03003 / 2.05 ( 286) hydrogen bonds : angle 4.73490 / 3.46 ( 828) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1427.57 seconds wall clock time: 25 minutes 0.85 seconds (1500.85 seconds total)