Starting phenix.real_space_refine on Wed Sep 17 05:56:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bt8_44881/09_2025/9bt8_44881.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bt8_44881/09_2025/9bt8_44881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9bt8_44881/09_2025/9bt8_44881.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bt8_44881/09_2025/9bt8_44881.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bt8_44881/09_2025/9bt8_44881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bt8_44881/09_2025/9bt8_44881.map" } resolution = 3.34 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= 0.055 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 16 5.16 5 C 3611 2.51 5 N 967 2.21 5 O 1112 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5712 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 439 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 2, 'TRANS': 52} Chain: "H" Number of atoms: 908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 908 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 2, 'TRANS': 114} Chain: "V" Number of atoms: 120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 120 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "A" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 849 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 2, 'TRANS': 108} Chain: "B" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2596 Classifications: {'peptide': 326} Link IDs: {'PTRANS': 21, 'TRANS': 304} Chain breaks: 3 Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 98} Time building chain proxies: 1.60, per 1000 atoms: 0.28 Number of scatterers: 5712 At special positions: 0 Unit cell: (60.48, 122.4, 102.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 6 15.00 O 1112 8.00 N 967 7.00 C 3611 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS C 95 " - pdb=" SG CYS B 120 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " 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: 0.49 Conformation dependent library (CDL) restraints added in 226.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1356 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 14 sheets defined 4.0% alpha, 42.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'H' and resid 31 through 33 No H-bonds generated for 'chain 'H' and resid 31 through 33' Processing helix chain 'H' and resid 90 through 94 removed outlier: 4.088A pdb=" N THR H 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.520A pdb=" N LYS A 64 " --> pdb=" O ASP A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 86 through 90 Processing helix chain 'B' and resid 98 through 109 Processing sheet with id=AA1, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AA2, first strand: chain 'C' and resid 108 through 110 Processing sheet with id=AA3, first strand: chain 'H' and resid 6 through 10 Processing sheet with id=AA4, first strand: chain 'H' and resid 61 through 63 removed outlier: 7.002A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N CYS H 99 " --> pdb=" O GLN H 115 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N GLN H 115 " --> pdb=" O CYS H 99 " (cutoff:3.500A) removed outlier: 7.556A pdb=" N ARG H 101 " --> pdb=" O TRP H 113 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N TRP H 113 " --> pdb=" O ARG H 101 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'V' and resid 361 through 364 Processing sheet with id=AA6, first strand: chain 'A' and resid 4 through 7 removed outlier: 4.215A pdb=" N GLN A 5 " --> pdb=" O VAL A 23 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL A 23 " --> pdb=" O GLN A 5 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N SER A 21 " --> pdb=" O SER A 7 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.532A pdb=" N THR A 111 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N MET A 34 " --> pdb=" O SER A 50 " (cutoff:3.500A) removed outlier: 4.854A pdb=" N SER A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.875A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 26 through 28 removed outlier: 3.875A pdb=" N TYR B 144 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N LYS B 170 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 9.819A pdb=" N VAL B 142 " --> pdb=" O LYS B 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 183 through 188 Processing sheet with id=AB2, first strand: chain 'B' and resid 207 through 208 removed outlier: 3.538A pdb=" N VAL B 343 " --> pdb=" O LEU B 327 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N TYR B 321 " --> pdb=" O PHE B 349 " (cutoff:3.500A) removed outlier: 7.450A pdb=" N LEU B 351 " --> pdb=" O VAL B 319 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N VAL B 319 " --> pdb=" O LEU B 351 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LYS B 230 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N GLN B 237 " --> pdb=" O PRO B 252 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N ALA B 239 " --> pdb=" O LYS B 250 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N LYS B 250 " --> pdb=" O ALA B 239 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N ILE B 241 " --> pdb=" O GLN B 248 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N GLN B 248 " --> pdb=" O ILE B 241 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 5 through 8 Processing sheet with id=AB4, first strand: chain 'L' and resid 11 through 13 removed outlier: 6.612A pdb=" N TRP L 36 " --> pdb=" O LEU L 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 11 through 13 removed outlier: 3.907A pdb=" N THR L 98 " --> pdb=" O GLN L 91 " (cutoff:3.500A) 218 hydrogen bonds defined for protein. 573 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: 0.89 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1829 1.34 - 1.46: 1411 1.46 - 1.58: 2547 1.58 - 1.70: 22 1.70 - 1.82: 23 Bond restraints: 5832 Sorted by residual: bond pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.717 1.606 0.111 2.00e-02 2.50e+03 3.06e+01 bond pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.05e+01 bond pdb=" O3P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" O2P TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 1.528 1.609 -0.081 2.00e-02 2.50e+03 1.63e+01 bond pdb=" O2P TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 1.528 1.608 -0.080 2.00e-02 2.50e+03 1.61e+01 ... (remaining 5827 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 7839 2.53 - 5.06: 68 5.06 - 7.59: 8 7.59 - 10.12: 4 10.12 - 12.65: 2 Bond angle restraints: 7921 Sorted by residual: angle pdb=" CB TPO V 359 " pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " ideal model delta sigma weight residual 119.31 106.66 12.65 3.00e+00 1.11e-01 1.78e+01 angle pdb=" CB TPO V 360 " pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " ideal model delta sigma weight residual 119.31 107.34 11.97 3.00e+00 1.11e-01 1.59e+01 angle pdb=" OG1 TPO V 360 " pdb=" P TPO V 360 " pdb=" O1P TPO V 360 " ideal model delta sigma weight residual 100.43 109.72 -9.29 3.00e+00 1.11e-01 9.59e+00 angle pdb=" CA TYR B 63 " pdb=" C TYR B 63 " pdb=" O TYR B 63 " ideal model delta sigma weight residual 119.08 122.16 -3.08 1.03e+00 9.43e-01 8.96e+00 angle pdb=" OG1 TPO V 359 " pdb=" P TPO V 359 " pdb=" O1P TPO V 359 " ideal model delta sigma weight residual 100.43 109.32 -8.89 3.00e+00 1.11e-01 8.79e+00 ... (remaining 7916 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 3016 17.83 - 35.66: 366 35.66 - 53.49: 78 53.49 - 71.32: 16 71.32 - 89.15: 6 Dihedral angle restraints: 3482 sinusoidal: 1367 harmonic: 2115 Sorted by residual: dihedral pdb=" CA VAL C 111 " pdb=" C VAL C 111 " pdb=" N ASN C 112 " pdb=" CA ASN C 112 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CB CYS C 95 " pdb=" SG CYS C 95 " pdb=" SG CYS B 120 " pdb=" CB CYS B 120 " ideal model delta sinusoidal sigma weight residual -86.00 -55.95 -30.05 1 1.00e+01 1.00e-02 1.29e+01 dihedral pdb=" CA LEU B 79 " pdb=" C LEU B 79 " pdb=" N PHE B 80 " pdb=" CA PHE B 80 " ideal model delta harmonic sigma weight residual 180.00 -162.58 -17.42 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 3479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 516 0.029 - 0.058: 243 0.058 - 0.087: 67 0.087 - 0.116: 45 0.116 - 0.144: 22 Chirality restraints: 893 Sorted by residual: chirality pdb=" CB VAL C 111 " pdb=" CA VAL C 111 " pdb=" CG1 VAL C 111 " pdb=" CG2 VAL C 111 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.14 2.00e-01 2.50e+01 5.22e-01 chirality pdb=" CA ILE L 49 " pdb=" N ILE L 49 " pdb=" C ILE L 49 " pdb=" CB ILE L 49 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ASP H 111 " pdb=" N ASP H 111 " pdb=" C ASP H 111 " pdb=" CB ASP H 111 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 ... (remaining 890 not shown) Planarity restraints: 1000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN H 16 " 0.044 5.00e-02 4.00e+02 6.62e-02 7.01e+00 pdb=" N PRO H 17 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO H 17 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 17 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 44 " 0.040 5.00e-02 4.00e+02 6.04e-02 5.84e+00 pdb=" N PRO B 45 " -0.104 5.00e-02 4.00e+02 pdb=" CA PRO B 45 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 45 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR H 107 " 0.006 2.00e-02 2.50e+03 1.22e-02 2.99e+00 pdb=" CG TYR H 107 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR H 107 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR H 107 " 0.013 2.00e-02 2.50e+03 pdb=" CE1 TYR H 107 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 TYR H 107 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR H 107 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR H 107 " -0.006 2.00e-02 2.50e+03 ... (remaining 997 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1411 2.79 - 3.32: 4562 3.32 - 3.85: 8562 3.85 - 4.37: 9874 4.37 - 4.90: 18352 Nonbonded interactions: 42761 Sorted by model distance: nonbonded pdb=" OG SER H 36 " pdb=" O ILE H 54 " model vdw 2.269 3.040 nonbonded pdb=" OG SER B 13 " pdb=" OD1 ASN B 15 " model vdw 2.292 3.040 nonbonded pdb=" O ALA B 263 " pdb=" OG SER B 266 " model vdw 2.317 3.040 nonbonded pdb=" O SER H 66 " pdb=" NH2 ARG H 70 " model vdw 2.325 3.120 nonbonded pdb=" ND2 ASN C 135 " pdb=" O ARG B 76 " model vdw 2.328 3.120 ... (remaining 42756 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: 1.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.390 Find NCS groups from input model: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 5835 Z= 0.227 Angle : 0.645 12.650 7927 Z= 0.318 Chirality : 0.043 0.144 893 Planarity : 0.005 0.066 1000 Dihedral : 16.428 89.153 2117 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.32 % Allowed : 25.44 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.32), residues: 700 helix: 1.19 (1.59), residues: 11 sheet: 0.48 (0.32), residues: 294 loop : -0.91 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 25 TYR 0.029 0.002 TYR H 107 PHE 0.012 0.001 PHE A 29 TRP 0.009 0.001 TRP H 50 HIS 0.005 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 5832) covalent geometry : angle 0.64482 ( 7921) SS BOND : bond 0.00043 ( 3) SS BOND : angle 0.38650 ( 6) hydrogen bonds : bond 0.25585 ( 207) hydrogen bonds : angle 10.00188 ( 573) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.218 Fit side-chains REVERT: H 107 TYR cc_start: 0.7548 (t80) cc_final: 0.7344 (t80) outliers start: 2 outliers final: 0 residues processed: 94 average time/residue: 0.0904 time to fit residues: 10.9495 Evaluate side-chains 91 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.112976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.092812 restraints weight = 8110.446| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.30 r_work: 0.2833 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2699 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5835 Z= 0.227 Angle : 0.632 8.911 7927 Z= 0.332 Chirality : 0.046 0.159 893 Planarity : 0.005 0.050 1000 Dihedral : 4.780 22.152 810 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.19 % Allowed : 25.76 % Favored : 70.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.32), residues: 700 helix: 1.48 (1.72), residues: 11 sheet: 0.65 (0.33), residues: 278 loop : -1.07 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 100 TYR 0.024 0.002 TYR C 136 PHE 0.016 0.002 PHE H 105 TRP 0.014 0.002 TRP H 50 HIS 0.007 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 5832) covalent geometry : angle 0.63174 ( 7921) SS BOND : bond 0.00090 ( 3) SS BOND : angle 0.68168 ( 6) hydrogen bonds : bond 0.04412 ( 207) hydrogen bonds : angle 6.59804 ( 573) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 90 time to evaluate : 0.234 Fit side-chains REVERT: B 110 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7984 (tm-30) REVERT: B 232 LYS cc_start: 0.8350 (mtpp) cc_final: 0.8008 (mttp) REVERT: L 80 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.8229 (mt0) outliers start: 26 outliers final: 20 residues processed: 111 average time/residue: 0.0948 time to fit residues: 13.3998 Evaluate side-chains 105 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 84 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 33 LEU Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 40 optimal weight: 1.9990 chunk 9 optimal weight: 0.0970 chunk 44 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 62 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.095046 restraints weight = 7898.874| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.45 r_work: 0.2960 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5835 Z= 0.161 Angle : 0.567 8.751 7927 Z= 0.297 Chirality : 0.044 0.148 893 Planarity : 0.004 0.035 1000 Dihedral : 4.605 20.742 810 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.70 % Allowed : 25.60 % Favored : 70.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.32), residues: 700 helix: 1.31 (1.72), residues: 11 sheet: 0.64 (0.32), residues: 296 loop : -1.09 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 25 TYR 0.019 0.001 TYR C 136 PHE 0.013 0.001 PHE A 29 TRP 0.011 0.001 TRP H 50 HIS 0.006 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00387 ( 5832) covalent geometry : angle 0.56713 ( 7921) SS BOND : bond 0.00225 ( 3) SS BOND : angle 0.91979 ( 6) hydrogen bonds : bond 0.03702 ( 207) hydrogen bonds : angle 6.03904 ( 573) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.228 Fit side-chains REVERT: C 92 TYR cc_start: 0.8830 (t80) cc_final: 0.8597 (t80) REVERT: H 107 TYR cc_start: 0.7526 (t80) cc_final: 0.7185 (t80) REVERT: B 110 GLU cc_start: 0.8389 (tm-30) cc_final: 0.8050 (tm-30) REVERT: B 232 LYS cc_start: 0.8275 (mtpp) cc_final: 0.7961 (mttt) REVERT: B 244 PHE cc_start: 0.8847 (m-10) cc_final: 0.8627 (m-10) REVERT: L 80 GLN cc_start: 0.8403 (OUTLIER) cc_final: 0.8092 (mt0) outliers start: 23 outliers final: 16 residues processed: 105 average time/residue: 0.0980 time to fit residues: 13.0324 Evaluate side-chains 103 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.0970 chunk 30 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 64 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 12 optimal weight: 0.0040 overall best weight: 0.5392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.118314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.097204 restraints weight = 8015.924| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 2.49 r_work: 0.2861 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 5835 Z= 0.129 Angle : 0.525 8.655 7927 Z= 0.273 Chirality : 0.042 0.142 893 Planarity : 0.004 0.040 1000 Dihedral : 4.386 22.336 810 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 5.15 % Allowed : 24.96 % Favored : 69.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.31), residues: 700 helix: 1.21 (1.71), residues: 11 sheet: 0.73 (0.32), residues: 296 loop : -1.09 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 25 TYR 0.016 0.001 TYR C 136 PHE 0.014 0.001 PHE A 29 TRP 0.010 0.001 TRP H 50 HIS 0.005 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 5832) covalent geometry : angle 0.52475 ( 7921) SS BOND : bond 0.00142 ( 3) SS BOND : angle 0.73071 ( 6) hydrogen bonds : bond 0.03158 ( 207) hydrogen bonds : angle 5.66956 ( 573) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 86 time to evaluate : 0.273 Fit side-chains REVERT: C 92 TYR cc_start: 0.8762 (t80) cc_final: 0.8518 (t80) REVERT: H 107 TYR cc_start: 0.7238 (t80) cc_final: 0.6871 (t80) REVERT: B 110 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7842 (tm-30) REVERT: B 232 LYS cc_start: 0.8073 (mtpp) cc_final: 0.7672 (mttp) REVERT: B 244 PHE cc_start: 0.8799 (m-10) cc_final: 0.8563 (m-10) REVERT: L 80 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7889 (mt0) outliers start: 32 outliers final: 24 residues processed: 111 average time/residue: 0.0884 time to fit residues: 12.6224 Evaluate side-chains 107 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 82 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 41 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.116300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.094591 restraints weight = 8065.167| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.59 r_work: 0.2927 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5835 Z= 0.219 Angle : 0.615 8.968 7927 Z= 0.319 Chirality : 0.045 0.136 893 Planarity : 0.005 0.044 1000 Dihedral : 4.744 21.707 810 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 6.76 % Allowed : 24.32 % Favored : 68.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.31), residues: 700 helix: 1.14 (1.70), residues: 11 sheet: 0.66 (0.33), residues: 284 loop : -1.23 (0.28), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 25 TYR 0.024 0.002 TYR C 136 PHE 0.016 0.002 PHE H 105 TRP 0.011 0.002 TRP H 50 HIS 0.007 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00535 ( 5832) covalent geometry : angle 0.61498 ( 7921) SS BOND : bond 0.00068 ( 3) SS BOND : angle 0.58862 ( 6) hydrogen bonds : bond 0.03656 ( 207) hydrogen bonds : angle 5.73392 ( 573) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 85 time to evaluate : 0.170 Fit side-chains REVERT: H 107 TYR cc_start: 0.7631 (t80) cc_final: 0.7346 (t80) REVERT: A 46 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7660 (mt-10) REVERT: A 69 ILE cc_start: 0.9011 (OUTLIER) cc_final: 0.8808 (tt) REVERT: B 110 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7864 (tm-30) REVERT: B 232 LYS cc_start: 0.8000 (mtpp) cc_final: 0.7581 (mttp) REVERT: B 244 PHE cc_start: 0.8830 (m-10) cc_final: 0.8514 (m-10) REVERT: L 80 GLN cc_start: 0.8360 (OUTLIER) cc_final: 0.8000 (mt0) outliers start: 42 outliers final: 33 residues processed: 121 average time/residue: 0.0904 time to fit residues: 13.9830 Evaluate side-chains 119 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 32 VAL Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 ASP Chi-restraints excluded: chain A residue 69 ILE Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 22 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.0060 chunk 3 optimal weight: 0.5980 chunk 61 optimal weight: 0.6980 chunk 25 optimal weight: 0.0040 chunk 38 optimal weight: 0.6980 overall best weight: 0.4008 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.096328 restraints weight = 7978.632| |-----------------------------------------------------------------------------| r_work (start): 0.3180 rms_B_bonded: 2.39 r_work: 0.3073 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5835 Z= 0.108 Angle : 0.508 8.539 7927 Z= 0.262 Chirality : 0.042 0.141 893 Planarity : 0.004 0.049 1000 Dihedral : 4.379 26.296 810 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.35 % Allowed : 27.86 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.31), residues: 700 helix: 1.13 (1.70), residues: 11 sheet: 0.74 (0.32), residues: 296 loop : -1.10 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 25 TYR 0.015 0.001 TYR C 136 PHE 0.014 0.001 PHE A 29 TRP 0.010 0.001 TRP H 50 HIS 0.004 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 5832) covalent geometry : angle 0.50788 ( 7921) SS BOND : bond 0.00133 ( 3) SS BOND : angle 0.49188 ( 6) hydrogen bonds : bond 0.02885 ( 207) hydrogen bonds : angle 5.41132 ( 573) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 84 time to evaluate : 0.203 Fit side-chains REVERT: C 122 HIS cc_start: 0.6779 (p90) cc_final: 0.6398 (p-80) REVERT: H 107 TYR cc_start: 0.7347 (t80) cc_final: 0.6861 (t80) REVERT: B 110 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8074 (tm-30) REVERT: B 232 LYS cc_start: 0.8225 (mtpp) cc_final: 0.7913 (mttp) REVERT: L 80 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.7899 (mt0) outliers start: 27 outliers final: 26 residues processed: 107 average time/residue: 0.0773 time to fit residues: 10.9060 Evaluate side-chains 108 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 81 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 34 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 61 optimal weight: 0.8980 chunk 40 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.0030 chunk 37 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.117200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.096189 restraints weight = 7986.535| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 2.45 r_work: 0.2881 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2737 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 5835 Z= 0.148 Angle : 0.545 8.656 7927 Z= 0.280 Chirality : 0.043 0.138 893 Planarity : 0.004 0.054 1000 Dihedral : 4.483 28.137 810 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 5.80 % Allowed : 26.41 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.31), residues: 700 helix: 1.30 (1.73), residues: 11 sheet: 0.75 (0.32), residues: 296 loop : -1.15 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG L 25 TYR 0.018 0.001 TYR C 136 PHE 0.013 0.001 PHE A 29 TRP 0.010 0.001 TRP H 50 HIS 0.005 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5832) covalent geometry : angle 0.54462 ( 7921) SS BOND : bond 0.00088 ( 3) SS BOND : angle 0.54791 ( 6) hydrogen bonds : bond 0.03097 ( 207) hydrogen bonds : angle 5.37980 ( 573) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 82 time to evaluate : 0.232 Fit side-chains REVERT: H 107 TYR cc_start: 0.7436 (t80) cc_final: 0.6902 (t80) REVERT: A 46 GLU cc_start: 0.8174 (OUTLIER) cc_final: 0.7948 (mt-10) REVERT: B 110 GLU cc_start: 0.8317 (tm-30) cc_final: 0.7987 (tm-30) REVERT: B 232 LYS cc_start: 0.8298 (mtpp) cc_final: 0.7958 (mttt) REVERT: L 80 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7965 (mt0) outliers start: 36 outliers final: 32 residues processed: 113 average time/residue: 0.0760 time to fit residues: 11.2762 Evaluate side-chains 115 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 81 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 28 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.0870 chunk 56 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.096372 restraints weight = 7988.702| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.46 r_work: 0.2995 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 5835 Z= 0.154 Angle : 0.545 8.667 7927 Z= 0.281 Chirality : 0.043 0.169 893 Planarity : 0.004 0.058 1000 Dihedral : 4.539 30.649 810 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 6.44 % Allowed : 25.76 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.31), residues: 700 helix: 1.31 (1.73), residues: 11 sheet: 0.78 (0.32), residues: 296 loop : -1.17 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 25 TYR 0.018 0.001 TYR C 136 PHE 0.013 0.001 PHE A 29 TRP 0.010 0.001 TRP H 50 HIS 0.005 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 5832) covalent geometry : angle 0.54524 ( 7921) SS BOND : bond 0.00087 ( 3) SS BOND : angle 0.58032 ( 6) hydrogen bonds : bond 0.03087 ( 207) hydrogen bonds : angle 5.37910 ( 573) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 85 time to evaluate : 0.216 Fit side-chains REVERT: H 107 TYR cc_start: 0.7432 (t80) cc_final: 0.6925 (t80) REVERT: A 43 LYS cc_start: 0.8745 (ttmm) cc_final: 0.8442 (mtpp) REVERT: A 46 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7960 (mt-10) REVERT: A 69 ILE cc_start: 0.8859 (tt) cc_final: 0.8606 (tt) REVERT: B 110 GLU cc_start: 0.8283 (tm-30) cc_final: 0.7969 (tm-30) REVERT: B 232 LYS cc_start: 0.8320 (mtpp) cc_final: 0.8013 (mttt) REVERT: L 80 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7980 (mt0) outliers start: 40 outliers final: 35 residues processed: 120 average time/residue: 0.0810 time to fit residues: 12.7522 Evaluate side-chains 120 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 83 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 14 LEU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 53 VAL Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 19 ARG Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 8 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.0980 chunk 46 optimal weight: 0.0970 chunk 54 optimal weight: 0.1980 chunk 63 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.117694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.096853 restraints weight = 7905.522| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.39 r_work: 0.2907 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5835 Z= 0.104 Angle : 0.515 8.468 7927 Z= 0.264 Chirality : 0.042 0.142 893 Planarity : 0.004 0.061 1000 Dihedral : 4.403 35.786 810 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 5.64 % Allowed : 26.57 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.31), residues: 700 helix: 1.36 (1.73), residues: 11 sheet: 0.85 (0.31), residues: 296 loop : -1.11 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG L 25 TYR 0.019 0.001 TYR B 63 PHE 0.013 0.001 PHE A 29 TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00245 ( 5832) covalent geometry : angle 0.51461 ( 7921) SS BOND : bond 0.00142 ( 3) SS BOND : angle 0.53281 ( 6) hydrogen bonds : bond 0.02790 ( 207) hydrogen bonds : angle 5.21005 ( 573) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.226 Fit side-chains REVERT: C 122 HIS cc_start: 0.6624 (p90) cc_final: 0.6242 (p-80) REVERT: H 107 TYR cc_start: 0.7470 (t80) cc_final: 0.6844 (t80) REVERT: A 43 LYS cc_start: 0.8736 (ttmm) cc_final: 0.8445 (mtpp) REVERT: A 46 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: A 69 ILE cc_start: 0.8834 (tt) cc_final: 0.8586 (tt) REVERT: B 110 GLU cc_start: 0.8406 (tm-30) cc_final: 0.8064 (tm-30) REVERT: B 232 LYS cc_start: 0.8296 (mtpp) cc_final: 0.8000 (mttt) REVERT: L 80 GLN cc_start: 0.8276 (OUTLIER) cc_final: 0.7854 (mt0) outliers start: 35 outliers final: 31 residues processed: 114 average time/residue: 0.0793 time to fit residues: 11.9004 Evaluate side-chains 117 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 84 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 62 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 64 optimal weight: 0.0870 chunk 65 optimal weight: 0.9980 chunk 1 optimal weight: 0.0870 chunk 54 optimal weight: 0.0670 chunk 57 optimal weight: 2.9990 overall best weight: 0.3674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 353 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.118425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.097797 restraints weight = 7962.145| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.33 r_work: 0.2996 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 5835 Z= 0.105 Angle : 0.514 8.524 7927 Z= 0.263 Chirality : 0.042 0.141 893 Planarity : 0.004 0.063 1000 Dihedral : 4.411 40.339 810 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.64 % Allowed : 26.09 % Favored : 68.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.32), residues: 700 helix: 1.32 (1.73), residues: 11 sheet: 0.77 (0.31), residues: 309 loop : -1.03 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 25 TYR 0.017 0.001 TYR B 63 PHE 0.013 0.001 PHE A 29 TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS C 122 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 5832) covalent geometry : angle 0.51435 ( 7921) SS BOND : bond 0.00134 ( 3) SS BOND : angle 0.51775 ( 6) hydrogen bonds : bond 0.02722 ( 207) hydrogen bonds : angle 5.10908 ( 573) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1400 Ramachandran restraints generated. 700 Oldfield, 0 Emsley, 700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 86 time to evaluate : 0.208 Fit side-chains REVERT: C 122 HIS cc_start: 0.6605 (p90) cc_final: 0.6285 (p-80) REVERT: A 46 GLU cc_start: 0.8234 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: A 69 ILE cc_start: 0.8862 (tt) cc_final: 0.8633 (tt) REVERT: B 110 GLU cc_start: 0.8591 (tm-30) cc_final: 0.8315 (tm-30) REVERT: B 232 LYS cc_start: 0.8278 (mtpp) cc_final: 0.8030 (mttt) REVERT: L 80 GLN cc_start: 0.8235 (OUTLIER) cc_final: 0.7765 (mt0) outliers start: 35 outliers final: 32 residues processed: 115 average time/residue: 0.0751 time to fit residues: 11.4089 Evaluate side-chains 119 residues out of total 621 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 126 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 92 GLU Chi-restraints excluded: chain H residue 110 LEU Chi-restraints excluded: chain A residue 4 LEU Chi-restraints excluded: chain A residue 12 VAL Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 24 VAL Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 72 ASP Chi-restraints excluded: chain A residue 76 ASN Chi-restraints excluded: chain A residue 78 VAL Chi-restraints excluded: chain B residue 47 TYR Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 220 VAL Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 298 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 23 THR Chi-restraints excluded: chain L residue 80 GLN Chi-restraints excluded: chain L residue 95 VAL Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 50 optimal weight: 2.9990 chunk 43 optimal weight: 0.0470 chunk 10 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 26 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 57 optimal weight: 0.0000 chunk 69 optimal weight: 0.0970 chunk 14 optimal weight: 0.8980 overall best weight: 0.2080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.121081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.099820 restraints weight = 7734.610| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.45 r_work: 0.2984 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5835 Z= 0.084 Angle : 0.488 8.331 7927 Z= 0.248 Chirality : 0.041 0.140 893 Planarity : 0.004 0.062 1000 Dihedral : 4.285 45.193 810 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 4.83 % Allowed : 27.38 % Favored : 67.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.32), residues: 700 helix: 1.27 (1.70), residues: 11 sheet: 0.89 (0.31), residues: 304 loop : -0.96 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 25 TYR 0.017 0.001 TYR B 63 PHE 0.012 0.001 PHE A 29 TRP 0.011 0.001 TRP H 106 HIS 0.002 0.000 HIS B 210 Details of bonding type rmsd covalent geometry : bond 0.00193 ( 5832) covalent geometry : angle 0.48821 ( 7921) SS BOND : bond 0.00177 ( 3) SS BOND : angle 0.55316 ( 6) hydrogen bonds : bond 0.02461 ( 207) hydrogen bonds : angle 4.92674 ( 573) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.24 seconds wall clock time: 27 minutes 59.66 seconds (1679.66 seconds total)