Starting phenix.real_space_refine on Wed Mar 5 19:43:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8adu_15370/03_2025/8adu_15370.cif Found real_map, /net/cci-nas-00/data/ceres_data/8adu_15370/03_2025/8adu_15370.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8adu_15370/03_2025/8adu_15370.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8adu_15370/03_2025/8adu_15370.map" model { file = "/net/cci-nas-00/data/ceres_data/8adu_15370/03_2025/8adu_15370.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8adu_15370/03_2025/8adu_15370.cif" } resolution = 3.24 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.001 sd= 0.008 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 10 5.16 5 C 2160 2.51 5 N 600 2.21 5 O 690 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3460 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 692 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 692 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Restraints were copied for chains: C, B, E, D Time building chain proxies: 1.83, per 1000 atoms: 0.53 Number of scatterers: 3460 At special positions: 0 Unit cell: (86.1, 97.65, 39.9, 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 10 16.00 O 690 8.00 N 600 7.00 C 2160 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.92 Conformation dependent library (CDL) restraints added in 467.3 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 850 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 27.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.880A pdb=" N ALA A 17 " --> pdb=" O ALA B 18 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU B 20 " --> pdb=" O ALA A 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA A 19 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA B 17 " --> pdb=" O ALA C 18 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU C 20 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA B 19 " --> pdb=" O GLU C 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA C 17 " --> pdb=" O ALA D 18 " (cutoff:3.500A) removed outlier: 8.102A pdb=" N GLU D 20 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA C 19 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N ALA D 17 " --> pdb=" O ALA E 18 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N GLU E 20 " --> pdb=" O ALA D 17 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ALA D 19 " --> pdb=" O GLU E 20 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 Processing sheet with id=AA3, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA4, first strand: chain 'A' and resid 48 through 54 Processing sheet with id=AA5, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.207A pdb=" N GLN A 62 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N ASN B 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR A 64 " --> pdb=" O ASN B 65 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN C 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR B 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N GLN C 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.753A pdb=" N ASN D 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N THR C 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N GLN D 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N ASN E 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N THR D 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 71 Processing sheet with id=AA7, first strand: chain 'A' and resid 75 through 78 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 94 76 hydrogen bonds defined for protein. 228 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: 0.79 Time building geometry restraints manager: 1.01 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: 1145 1.34 - 1.45: 439 1.45 - 1.57: 1871 1.57 - 1.69: 0 1.69 - 1.80: 20 Bond restraints: 3475 Sorted by residual: bond pdb=" CB VAL E 15 " pdb=" CG2 VAL E 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.70e+00 bond pdb=" CB VAL A 15 " pdb=" CG2 VAL A 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.69e+00 bond pdb=" CB VAL D 15 " pdb=" CG2 VAL D 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL C 15 " pdb=" CG2 VAL C 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.67e+00 bond pdb=" CB VAL B 15 " pdb=" CG2 VAL B 15 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.66e+00 ... (remaining 3470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 3777 0.88 - 1.77: 660 1.77 - 2.65: 153 2.65 - 3.53: 45 3.53 - 4.42: 25 Bond angle restraints: 4660 Sorted by residual: angle pdb=" CA GLN D 79 " pdb=" CB GLN D 79 " pdb=" CG GLN D 79 " ideal model delta sigma weight residual 114.10 118.52 -4.42 2.00e+00 2.50e-01 4.87e+00 angle pdb=" CA GLN A 79 " pdb=" CB GLN A 79 " pdb=" CG GLN A 79 " ideal model delta sigma weight residual 114.10 118.51 -4.41 2.00e+00 2.50e-01 4.86e+00 angle pdb=" C GLN E 79 " pdb=" CA GLN E 79 " pdb=" CB GLN E 79 " ideal model delta sigma weight residual 110.42 114.81 -4.39 1.99e+00 2.53e-01 4.86e+00 angle pdb=" CA GLN C 79 " pdb=" CB GLN C 79 " pdb=" CG GLN C 79 " ideal model delta sigma weight residual 114.10 118.50 -4.40 2.00e+00 2.50e-01 4.85e+00 angle pdb=" C GLN C 79 " pdb=" CA GLN C 79 " pdb=" CB GLN C 79 " ideal model delta sigma weight residual 110.42 114.80 -4.38 1.99e+00 2.53e-01 4.85e+00 ... (remaining 4655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.35: 1904 17.35 - 34.69: 136 34.69 - 52.03: 30 52.03 - 69.38: 5 69.38 - 86.72: 15 Dihedral angle restraints: 2090 sinusoidal: 745 harmonic: 1345 Sorted by residual: dihedral pdb=" CA MET E 5 " pdb=" C MET E 5 " pdb=" N LYS E 6 " pdb=" CA LYS E 6 " ideal model delta harmonic sigma weight residual 180.00 -160.26 -19.74 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET D 5 " pdb=" C MET D 5 " pdb=" N LYS D 6 " pdb=" CA LYS D 6 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA MET C 5 " pdb=" C MET C 5 " pdb=" N LYS C 6 " pdb=" CA LYS C 6 " ideal model delta harmonic sigma weight residual -180.00 -160.27 -19.73 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 2087 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 505 0.087 - 0.173: 65 0.173 - 0.260: 5 0.260 - 0.347: 0 0.347 - 0.433: 5 Chirality restraints: 580 Sorted by residual: chirality pdb=" CB VAL D 15 " pdb=" CA VAL D 15 " pdb=" CG1 VAL D 15 " pdb=" CG2 VAL D 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CB VAL E 15 " pdb=" CA VAL E 15 " pdb=" CG1 VAL E 15 " pdb=" CG2 VAL E 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.65e+00 chirality pdb=" CB VAL B 15 " pdb=" CA VAL B 15 " pdb=" CG1 VAL B 15 " pdb=" CG2 VAL B 15 " both_signs ideal model delta sigma weight residual False -2.63 -2.20 -0.43 2.00e-01 2.50e+01 4.65e+00 ... (remaining 577 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE E 4 " -0.010 2.00e-02 2.50e+03 9.37e-03 1.54e+00 pdb=" CG PHE E 4 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE E 4 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE E 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE E 4 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE E 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE E 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 4 " -0.010 2.00e-02 2.50e+03 9.22e-03 1.49e+00 pdb=" CG PHE D 4 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE D 4 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE D 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE D 4 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE D 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE D 4 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 4 " -0.010 2.00e-02 2.50e+03 9.20e-03 1.48e+00 pdb=" CG PHE C 4 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE C 4 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 4 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE C 4 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 4 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE C 4 " -0.003 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1071 2.82 - 3.34: 3134 3.34 - 3.86: 5731 3.86 - 4.38: 6806 4.38 - 4.90: 13256 Nonbonded interactions: 29998 Sorted by model distance: nonbonded pdb=" OG SER E 9 " pdb=" N LYS E 10 " model vdw 2.296 3.120 nonbonded pdb=" OG SER C 9 " pdb=" N LYS C 10 " model vdw 2.297 3.120 nonbonded pdb=" OG SER D 9 " pdb=" N LYS D 10 " model vdw 2.297 3.120 nonbonded pdb=" OG SER A 9 " pdb=" N LYS A 10 " model vdw 2.297 3.120 nonbonded pdb=" OG SER B 9 " pdb=" N LYS B 10 " model vdw 2.297 3.120 ... (remaining 29993 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.450 Find NCS groups from input model: 0.080 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 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 : 0.007 0.057 3475 Z= 0.458 Angle : 0.820 4.415 4660 Z= 0.461 Chirality : 0.068 0.433 580 Planarity : 0.003 0.009 585 Dihedral : 15.523 86.720 1240 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.34 % Favored : 88.66 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.25), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.19), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS C 50 PHE 0.022 0.005 PHE E 4 TYR 0.005 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 LYS cc_start: 0.7926 (tttm) cc_final: 0.7706 (ttmm) REVERT: B 99 GLN cc_start: 0.4969 (tm-30) cc_final: 0.4709 (tm-30) REVERT: C 12 LYS cc_start: 0.7500 (mptt) cc_final: 0.7264 (mptt) REVERT: C 60 LYS cc_start: 0.7879 (tttm) cc_final: 0.7641 (ttmm) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1390 time to fit residues: 15.3753 Evaluate side-chains 69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 37 optimal weight: 5.9990 chunk 34 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 35 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.109123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.092972 restraints weight = 5015.193| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.48 r_work: 0.3394 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3475 Z= 0.320 Angle : 0.695 7.378 4660 Z= 0.369 Chirality : 0.051 0.172 580 Planarity : 0.003 0.010 585 Dihedral : 5.141 15.745 495 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 5.51 % Allowed : 15.94 % Favored : 78.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.47 (0.28), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.21), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.019 0.004 PHE D 4 TYR 0.014 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.378 Fit side-chains REVERT: A 60 LYS cc_start: 0.7878 (tttm) cc_final: 0.7520 (ttmm) REVERT: B 60 LYS cc_start: 0.7835 (tttm) cc_final: 0.7456 (ttmm) REVERT: C 60 LYS cc_start: 0.7789 (tttm) cc_final: 0.7443 (ttmm) REVERT: D 60 LYS cc_start: 0.7891 (tttm) cc_final: 0.7422 (ttmm) outliers start: 19 outliers final: 14 residues processed: 88 average time/residue: 0.1328 time to fit residues: 14.6562 Evaluate side-chains 87 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 17 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 7 optimal weight: 0.0470 chunk 30 optimal weight: 6.9990 chunk 28 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 chunk 37 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 overall best weight: 4.0086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.105855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.089856 restraints weight = 5085.717| |-----------------------------------------------------------------------------| r_work (start): 0.3457 rms_B_bonded: 2.49 r_work: 0.3353 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3235 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 3475 Z= 0.411 Angle : 0.724 6.633 4660 Z= 0.385 Chirality : 0.052 0.152 580 Planarity : 0.003 0.010 585 Dihedral : 5.451 17.718 495 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.75 % Favored : 88.25 % Rotamer: Outliers : 6.96 % Allowed : 16.81 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.44 (0.28), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.021 0.005 PHE B 94 TYR 0.010 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.407 Fit side-chains REVERT: A 60 LYS cc_start: 0.7880 (tttm) cc_final: 0.7547 (ttmm) REVERT: B 60 LYS cc_start: 0.7823 (tttm) cc_final: 0.7481 (ttmm) REVERT: C 60 LYS cc_start: 0.7801 (tttm) cc_final: 0.7465 (ttmm) REVERT: D 60 LYS cc_start: 0.8008 (tttm) cc_final: 0.7588 (ttmm) outliers start: 24 outliers final: 17 residues processed: 96 average time/residue: 0.1323 time to fit residues: 15.8598 Evaluate side-chains 90 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 41 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 40 optimal weight: 9.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.109641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.093530 restraints weight = 5036.688| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.53 r_work: 0.3414 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3297 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3475 Z= 0.294 Angle : 0.654 7.119 4660 Z= 0.348 Chirality : 0.050 0.139 580 Planarity : 0.003 0.010 585 Dihedral : 5.039 16.112 495 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 6.67 % Allowed : 17.39 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.019 0.005 PHE C 94 TYR 0.008 0.003 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.404 Fit side-chains REVERT: A 10 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7659 (ptpp) REVERT: A 60 LYS cc_start: 0.7865 (tttm) cc_final: 0.7527 (ttmm) REVERT: B 60 LYS cc_start: 0.7861 (tttm) cc_final: 0.7490 (ttmm) REVERT: C 10 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7337 (ptpp) REVERT: C 60 LYS cc_start: 0.7807 (tttm) cc_final: 0.7461 (ttmm) REVERT: D 60 LYS cc_start: 0.8013 (tttm) cc_final: 0.7587 (ttmm) outliers start: 23 outliers final: 20 residues processed: 95 average time/residue: 0.1684 time to fit residues: 19.1720 Evaluate side-chains 96 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 40 optimal weight: 8.9990 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 7 optimal weight: 0.4980 overall best weight: 3.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** 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 = 0.3710 r_free = 0.3710 target = 0.108910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.092722 restraints weight = 5082.619| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.52 r_work: 0.3399 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3282 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3282 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 3475 Z= 0.328 Angle : 0.667 6.703 4660 Z= 0.354 Chirality : 0.050 0.142 580 Planarity : 0.003 0.011 585 Dihedral : 5.073 16.963 495 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.13 % Favored : 88.87 % Rotamer: Outliers : 7.54 % Allowed : 18.84 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.020 0.005 PHE C 94 TYR 0.022 0.004 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.373 Fit side-chains REVERT: A 60 LYS cc_start: 0.7866 (tttm) cc_final: 0.7531 (ttmm) REVERT: B 60 LYS cc_start: 0.7885 (tttm) cc_final: 0.7523 (ttmm) REVERT: C 10 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7378 (ptpp) REVERT: C 60 LYS cc_start: 0.7826 (tttm) cc_final: 0.7492 (ttmm) REVERT: D 60 LYS cc_start: 0.7956 (tttm) cc_final: 0.7378 (tttm) outliers start: 26 outliers final: 24 residues processed: 95 average time/residue: 0.1722 time to fit residues: 19.5355 Evaluate side-chains 100 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 28 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 6 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 1 optimal weight: 10.0000 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** 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 = 0.3703 r_free = 0.3703 target = 0.108168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.091860 restraints weight = 5131.584| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.52 r_work: 0.3387 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3475 Z= 0.358 Angle : 0.689 6.338 4660 Z= 0.365 Chirality : 0.051 0.145 580 Planarity : 0.003 0.010 585 Dihedral : 5.210 17.838 495 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.55 % Favored : 88.45 % Rotamer: Outliers : 8.12 % Allowed : 19.13 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.021 0.005 PHE B 94 TYR 0.019 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 0.413 Fit side-chains REVERT: A 60 LYS cc_start: 0.7875 (tttm) cc_final: 0.7545 (ttmm) REVERT: A 79 GLN cc_start: 0.7845 (OUTLIER) cc_final: 0.5238 (pt0) REVERT: B 60 LYS cc_start: 0.7892 (tttm) cc_final: 0.7528 (ttmm) REVERT: C 10 LYS cc_start: 0.7776 (OUTLIER) cc_final: 0.7422 (ptpp) REVERT: C 60 LYS cc_start: 0.7832 (tttm) cc_final: 0.7504 (ttmm) REVERT: D 60 LYS cc_start: 0.7964 (tttm) cc_final: 0.7394 (tttm) outliers start: 28 outliers final: 24 residues processed: 96 average time/residue: 0.1744 time to fit residues: 20.0999 Evaluate side-chains 103 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 77 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 15 VAL Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain A residue 81 THR Chi-restraints excluded: chain B residue 10 LYS Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 10 LYS Chi-restraints excluded: chain D residue 15 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 81 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 0.5980 chunk 12 optimal weight: 0.9990 chunk 23 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 79 GLN D 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.120487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.104056 restraints weight = 4807.861| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.50 r_work: 0.3595 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3479 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3479 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3475 Z= 0.145 Angle : 0.560 6.386 4660 Z= 0.296 Chirality : 0.048 0.139 580 Planarity : 0.002 0.010 585 Dihedral : 4.350 15.024 495 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.78 % Favored : 87.22 % Rotamer: Outliers : 6.38 % Allowed : 22.03 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.38 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.015 0.004 PHE C 94 TYR 0.011 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 87 time to evaluate : 0.421 Fit side-chains REVERT: A 12 LYS cc_start: 0.7651 (mptt) cc_final: 0.6804 (tppt) REVERT: A 60 LYS cc_start: 0.7850 (tttm) cc_final: 0.7511 (ttmm) REVERT: A 79 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.4893 (pt0) REVERT: B 60 LYS cc_start: 0.7830 (tttm) cc_final: 0.7267 (tttm) REVERT: C 60 LYS cc_start: 0.7879 (tttm) cc_final: 0.7565 (ttmm) REVERT: D 46 GLU cc_start: 0.9068 (pm20) cc_final: 0.8831 (pm20) REVERT: D 60 LYS cc_start: 0.7986 (tttm) cc_final: 0.6808 (tttm) REVERT: E 61 GLU cc_start: 0.7684 (mp0) cc_final: 0.6800 (mp0) outliers start: 22 outliers final: 15 residues processed: 101 average time/residue: 0.1561 time to fit residues: 19.2436 Evaluate side-chains 99 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 33 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 8.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.106243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.089833 restraints weight = 5154.763| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 2.50 r_work: 0.3375 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3254 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 3475 Z= 0.477 Angle : 0.766 6.487 4660 Z= 0.405 Chirality : 0.053 0.161 580 Planarity : 0.003 0.011 585 Dihedral : 5.342 18.364 495 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 6.96 % Allowed : 20.58 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.32 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.024 0.006 PHE C 94 TYR 0.017 0.003 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.426 Fit side-chains REVERT: A 60 LYS cc_start: 0.7848 (tttm) cc_final: 0.7551 (ttmm) REVERT: B 60 LYS cc_start: 0.7886 (tttm) cc_final: 0.7491 (ttmm) REVERT: C 5 MET cc_start: 0.7325 (ttt) cc_final: 0.6976 (ttt) REVERT: C 10 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7478 (ptpp) REVERT: C 60 LYS cc_start: 0.7876 (tttm) cc_final: 0.7565 (ttmm) REVERT: D 60 LYS cc_start: 0.7979 (tttm) cc_final: 0.7449 (tttm) outliers start: 24 outliers final: 17 residues processed: 94 average time/residue: 0.1599 time to fit residues: 18.5486 Evaluate side-chains 95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 81 THR Chi-restraints excluded: chain C residue 10 LYS Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 32 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.3831 r_free = 0.3831 target = 0.115875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.099313 restraints weight = 4758.676| |-----------------------------------------------------------------------------| r_work (start): 0.3628 rms_B_bonded: 2.48 r_work: 0.3526 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3475 Z= 0.196 Angle : 0.617 6.403 4660 Z= 0.325 Chirality : 0.049 0.142 580 Planarity : 0.002 0.010 585 Dihedral : 4.528 16.626 495 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.99 % Favored : 87.01 % Rotamer: Outliers : 5.22 % Allowed : 23.19 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.29), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.22), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.017 0.004 PHE C 94 TYR 0.014 0.002 TYR A 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 83 time to evaluate : 0.372 Fit side-chains REVERT: A 35 GLU cc_start: 0.8256 (tt0) cc_final: 0.7997 (mm-30) REVERT: A 60 LYS cc_start: 0.7844 (tttm) cc_final: 0.7483 (ttmm) REVERT: A 79 GLN cc_start: 0.7335 (OUTLIER) cc_final: 0.4970 (pt0) REVERT: B 35 GLU cc_start: 0.8685 (mt-10) cc_final: 0.8321 (mt-10) REVERT: B 60 LYS cc_start: 0.7834 (tttm) cc_final: 0.7464 (ttmm) REVERT: C 60 LYS cc_start: 0.7914 (tttm) cc_final: 0.7574 (ttmm) REVERT: D 12 LYS cc_start: 0.7228 (mptt) cc_final: 0.6942 (mptt) REVERT: D 46 GLU cc_start: 0.9088 (pm20) cc_final: 0.8863 (pm20) REVERT: D 60 LYS cc_start: 0.8031 (tttm) cc_final: 0.6798 (tttm) REVERT: E 61 GLU cc_start: 0.7704 (mp0) cc_final: 0.6995 (mp0) outliers start: 18 outliers final: 16 residues processed: 93 average time/residue: 0.1476 time to fit residues: 16.8278 Evaluate side-chains 100 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 3 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 42 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.107021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.090637 restraints weight = 4976.676| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.47 r_work: 0.3384 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3475 Z= 0.460 Angle : 0.774 7.294 4660 Z= 0.408 Chirality : 0.052 0.159 580 Planarity : 0.003 0.010 585 Dihedral : 5.293 19.326 495 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.16 % Favored : 87.84 % Rotamer: Outliers : 4.93 % Allowed : 23.19 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.33 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.024 0.006 PHE D 4 TYR 0.018 0.004 TYR A 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.366 Fit side-chains REVERT: A 60 LYS cc_start: 0.7855 (tttm) cc_final: 0.7588 (ttmm) REVERT: A 79 GLN cc_start: 0.8204 (OUTLIER) cc_final: 0.5259 (pt0) REVERT: B 60 LYS cc_start: 0.7871 (tttm) cc_final: 0.7479 (ttmm) REVERT: C 60 LYS cc_start: 0.7882 (tttm) cc_final: 0.7565 (ttmm) REVERT: D 12 LYS cc_start: 0.7316 (mptt) cc_final: 0.7097 (mptt) REVERT: D 60 LYS cc_start: 0.7982 (tttm) cc_final: 0.7435 (tttm) outliers start: 17 outliers final: 16 residues processed: 88 average time/residue: 0.1448 time to fit residues: 15.6595 Evaluate side-chains 93 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain A residue 79 GLN Chi-restraints excluded: chain B residue 15 VAL Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 42 SER Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 15 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 35 GLU Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 10 LYS Chi-restraints excluded: chain E residue 26 VAL Chi-restraints excluded: chain E residue 42 SER Chi-restraints excluded: chain E residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 44 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 8.9990 chunk 6 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 42 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3733 r_free = 0.3733 target = 0.108447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.091916 restraints weight = 5072.935| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 2.51 r_work: 0.3409 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 3475 Z= 0.376 Angle : 0.743 7.034 4660 Z= 0.392 Chirality : 0.051 0.151 580 Planarity : 0.003 0.010 585 Dihedral : 5.229 20.034 495 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 5.80 % Allowed : 22.90 % Favored : 71.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.34 (0.30), residues: 485 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.23), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.021 0.005 PHE C 94 TYR 0.017 0.003 TYR A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1941.81 seconds wall clock time: 34 minutes 30.09 seconds (2070.09 seconds total)