Starting phenix.real_space_refine on Wed Jul 23 08:51:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7v48_31703/07_2025/7v48_31703.cif Found real_map, /net/cci-nas-00/data/ceres_data/7v48_31703/07_2025/7v48_31703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7v48_31703/07_2025/7v48_31703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7v48_31703/07_2025/7v48_31703.map" model { file = "/net/cci-nas-00/data/ceres_data/7v48_31703/07_2025/7v48_31703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7v48_31703/07_2025/7v48_31703.cif" } resolution = 3.0 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= 0.000 sd= 0.006 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: 3 Type Number sf(0) Gaussians C 1626 2.51 5 N 450 2.21 5 O 522 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 2598 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 433 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Restraints were copied for chains: C, B, E, D, F Time building chain proxies: 1.66, per 1000 atoms: 0.64 Number of scatterers: 2598 At special positions: 0 Unit cell: (104.94, 110.24, 32.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 522 8.00 N 450 7.00 C 1626 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: 0.64 Conformation dependent library (CDL) restraints added in 449.0 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 636 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 9 sheets defined 0.0% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 38 through 40 removed outlier: 6.719A pdb=" N TYR B 39 " --> pdb=" O VAL F 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 48 through 50 removed outlier: 6.501A pdb=" N VAL B 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA4, first strand: chain 'E' and resid 75 through 79 removed outlier: 6.608A pdb=" N ALA B 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N GLN F 79 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 82 through 83 removed outlier: 6.541A pdb=" N VAL B 82 " --> pdb=" O GLU F 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 40 removed outlier: 6.748A pdb=" N TYR A 39 " --> pdb=" O VAL D 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 48 through 50 removed outlier: 6.513A pdb=" N VAL A 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 75 through 79 removed outlier: 6.603A pdb=" N ALA A 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.180A pdb=" N GLN D 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ALA A 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.549A pdb=" N VAL A 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) 19 hydrogen bonds defined for protein. 57 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: 0.52 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 456 1.29 - 1.36: 408 1.36 - 1.42: 102 1.42 - 1.49: 426 1.49 - 1.55: 1218 Bond restraints: 2610 Sorted by residual: bond pdb=" CA ALA D 90 " pdb=" C ALA D 90 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.10e-02 8.26e+03 4.74e-01 bond pdb=" CA ALA F 90 " pdb=" C ALA F 90 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.10e-02 8.26e+03 4.74e-01 bond pdb=" CA ALA A 90 " pdb=" C ALA A 90 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.10e-02 8.26e+03 4.70e-01 bond pdb=" CA ALA B 90 " pdb=" C ALA B 90 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.10e-02 8.26e+03 4.14e-01 bond pdb=" CA ALA E 90 " pdb=" C ALA E 90 " ideal model delta sigma weight residual 1.530 1.523 0.007 1.10e-02 8.26e+03 4.09e-01 ... (remaining 2605 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.55: 2848 0.55 - 1.10: 539 1.10 - 1.65: 103 1.65 - 2.21: 32 2.21 - 2.76: 6 Bond angle restraints: 3528 Sorted by residual: angle pdb=" CA ALA F 90 " pdb=" C ALA F 90 " pdb=" N ALA F 91 " ideal model delta sigma weight residual 114.76 116.75 -1.99 1.14e+00 7.69e-01 3.05e+00 angle pdb=" CA ALA D 90 " pdb=" C ALA D 90 " pdb=" N ALA D 91 " ideal model delta sigma weight residual 114.76 116.71 -1.95 1.14e+00 7.69e-01 2.94e+00 angle pdb=" CA ALA C 90 " pdb=" C ALA C 90 " pdb=" N ALA C 91 " ideal model delta sigma weight residual 114.76 116.69 -1.93 1.14e+00 7.69e-01 2.86e+00 angle pdb=" CA ALA A 90 " pdb=" C ALA A 90 " pdb=" N ALA A 91 " ideal model delta sigma weight residual 114.76 116.69 -1.93 1.14e+00 7.69e-01 2.86e+00 angle pdb=" CA ALA E 90 " pdb=" C ALA E 90 " pdb=" N ALA E 91 " ideal model delta sigma weight residual 114.76 116.68 -1.92 1.14e+00 7.69e-01 2.84e+00 ... (remaining 3523 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.21: 1350 13.21 - 26.41: 120 26.41 - 39.62: 36 39.62 - 52.82: 0 52.82 - 66.03: 12 Dihedral angle restraints: 1518 sinusoidal: 504 harmonic: 1014 Sorted by residual: dihedral pdb=" CA ASP B 98 " pdb=" CB ASP B 98 " pdb=" CG ASP B 98 " pdb=" OD1 ASP B 98 " ideal model delta sinusoidal sigma weight residual -30.00 -89.45 59.45 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP F 98 " pdb=" CB ASP F 98 " pdb=" CG ASP F 98 " pdb=" OD1 ASP F 98 " ideal model delta sinusoidal sigma weight residual -30.00 -89.44 59.44 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASP C 98 " pdb=" CB ASP C 98 " pdb=" CG ASP C 98 " pdb=" OD1 ASP C 98 " ideal model delta sinusoidal sigma weight residual -30.00 -89.41 59.41 1 2.00e+01 2.50e-03 1.18e+01 ... (remaining 1515 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 227 0.026 - 0.053: 128 0.053 - 0.079: 35 0.079 - 0.106: 37 0.106 - 0.132: 35 Chirality restraints: 462 Sorted by residual: chirality pdb=" CA VAL C 66 " pdb=" N VAL C 66 " pdb=" C VAL C 66 " pdb=" CB VAL C 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL D 66 " pdb=" N VAL D 66 " pdb=" C VAL D 66 " pdb=" CB VAL D 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.35e-01 chirality pdb=" CA VAL F 66 " pdb=" N VAL F 66 " pdb=" C VAL F 66 " pdb=" CB VAL F 66 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.30e-01 ... (remaining 459 not shown) Planarity restraints: 438 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 68 " 0.003 2.00e-02 2.50e+03 6.10e-03 3.72e-01 pdb=" C GLY B 68 " -0.011 2.00e-02 2.50e+03 pdb=" O GLY B 68 " 0.004 2.00e-02 2.50e+03 pdb=" N ALA B 69 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 68 " -0.003 2.00e-02 2.50e+03 6.08e-03 3.70e-01 pdb=" C GLY A 68 " 0.011 2.00e-02 2.50e+03 pdb=" O GLY A 68 " -0.004 2.00e-02 2.50e+03 pdb=" N ALA A 69 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 68 " -0.003 2.00e-02 2.50e+03 6.04e-03 3.65e-01 pdb=" C GLY D 68 " 0.010 2.00e-02 2.50e+03 pdb=" O GLY D 68 " -0.004 2.00e-02 2.50e+03 pdb=" N ALA D 69 " -0.004 2.00e-02 2.50e+03 ... (remaining 435 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 716 2.82 - 3.34: 2357 3.34 - 3.86: 3650 3.86 - 4.38: 4096 4.38 - 4.90: 8597 Nonbonded interactions: 19416 Sorted by model distance: nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.295 3.120 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN F 62 " pdb=" OG1 THR F 64 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.296 3.120 nonbonded pdb=" NE2 GLN D 62 " pdb=" OG1 THR D 64 " model vdw 2.296 3.120 ... (remaining 19411 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' selection = chain 'F' } 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: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 10.860 Find NCS groups from input model: 0.070 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:13.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 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 : 0.002 0.009 2610 Z= 0.109 Angle : 0.484 2.756 3528 Z= 0.293 Chirality : 0.051 0.132 462 Planarity : 0.001 0.006 438 Dihedral : 12.912 66.027 882 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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: -5.61 (0.29), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.27 (0.22), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 50 PHE 0.005 0.001 PHE C 94 TYR 0.009 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.18944 ( 19) hydrogen bonds : angle 8.14965 ( 57) covalent geometry : bond 0.00181 ( 2610) covalent geometry : angle 0.48380 ( 3528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.293 Fit side-chains REVERT: B 46 GLU cc_start: 0.6694 (tt0) cc_final: 0.5943 (tp30) REVERT: A 46 GLU cc_start: 0.6393 (tt0) cc_final: 0.5827 (tp30) REVERT: A 57 GLU cc_start: 0.7224 (tt0) cc_final: 0.6981 (mt-10) REVERT: E 43 LYS cc_start: 0.7369 (tttt) cc_final: 0.7013 (mtpp) REVERT: E 46 GLU cc_start: 0.7164 (tt0) cc_final: 0.6744 (tt0) REVERT: C 43 LYS cc_start: 0.7382 (tttt) cc_final: 0.7090 (mtpm) REVERT: C 46 GLU cc_start: 0.6823 (tt0) cc_final: 0.6023 (tp30) REVERT: F 43 LYS cc_start: 0.7784 (tttt) cc_final: 0.7579 (ttmm) REVERT: F 46 GLU cc_start: 0.6978 (tt0) cc_final: 0.6701 (tt0) REVERT: D 46 GLU cc_start: 0.7069 (tt0) cc_final: 0.6471 (tp30) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.9458 time to fit residues: 65.3183 Evaluate side-chains 47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN E 79 GLN C 79 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.158842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.115339 restraints weight = 2853.709| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.83 r_work: 0.3785 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2610 Z= 0.226 Angle : 0.568 3.653 3528 Z= 0.327 Chirality : 0.051 0.124 462 Planarity : 0.003 0.008 438 Dihedral : 5.101 15.265 378 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.95 % Favored : 80.05 % Rotamer: Outliers : 5.68 % Allowed : 9.47 % Favored : 84.85 % 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: -5.37 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.007 0.002 PHE A 94 TYR 0.013 0.004 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.02669 ( 19) hydrogen bonds : angle 5.03297 ( 57) covalent geometry : bond 0.00497 ( 2610) covalent geometry : angle 0.56765 ( 3528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 49 time to evaluate : 0.302 Fit side-chains REVERT: B 46 GLU cc_start: 0.7313 (tt0) cc_final: 0.6642 (tp30) REVERT: B 65 ASN cc_start: 0.7162 (t0) cc_final: 0.6949 (t0) REVERT: A 46 GLU cc_start: 0.7226 (tt0) cc_final: 0.6238 (tm-30) REVERT: A 92 THR cc_start: 0.7450 (m) cc_final: 0.7127 (p) REVERT: E 43 LYS cc_start: 0.7896 (tttt) cc_final: 0.7595 (mtpm) REVERT: E 46 GLU cc_start: 0.7713 (tt0) cc_final: 0.6905 (tm-30) REVERT: E 92 THR cc_start: 0.7554 (m) cc_final: 0.7066 (p) REVERT: C 43 LYS cc_start: 0.7862 (tttt) cc_final: 0.7594 (mtpm) REVERT: C 46 GLU cc_start: 0.7492 (tt0) cc_final: 0.6757 (tp30) REVERT: F 46 GLU cc_start: 0.7452 (tt0) cc_final: 0.7207 (tt0) REVERT: F 57 GLU cc_start: 0.8046 (tt0) cc_final: 0.7808 (tt0) REVERT: D 46 GLU cc_start: 0.7717 (tt0) cc_final: 0.6980 (tp30) REVERT: D 62 GLN cc_start: 0.7349 (tp40) cc_final: 0.7009 (tm-30) outliers start: 15 outliers final: 9 residues processed: 61 average time/residue: 0.9584 time to fit residues: 60.1646 Evaluate side-chains 49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 54 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 13 optimal weight: 5.9990 chunk 24 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 14 optimal weight: 0.0370 chunk 26 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 overall best weight: 0.6860 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.167537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.123943 restraints weight = 2726.571| |-----------------------------------------------------------------------------| r_work (start): 0.4044 rms_B_bonded: 2.81 r_work: 0.3901 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2610 Z= 0.077 Angle : 0.433 3.678 3528 Z= 0.239 Chirality : 0.050 0.128 462 Planarity : 0.001 0.005 438 Dihedral : 4.153 11.835 378 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 3.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.29 % Favored : 90.71 % Rotamer: Outliers : 2.65 % Allowed : 13.26 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.76 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.004 0.001 PHE A 94 TYR 0.003 0.001 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.01341 ( 19) hydrogen bonds : angle 3.89856 ( 57) covalent geometry : bond 0.00162 ( 2610) covalent geometry : angle 0.43298 ( 3528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.275 Fit side-chains REVERT: B 46 GLU cc_start: 0.7332 (tt0) cc_final: 0.6495 (tp30) REVERT: A 46 GLU cc_start: 0.7134 (tt0) cc_final: 0.6120 (tp30) REVERT: E 43 LYS cc_start: 0.7662 (tttt) cc_final: 0.7386 (mtpm) REVERT: E 46 GLU cc_start: 0.7669 (tt0) cc_final: 0.7230 (tt0) REVERT: E 92 THR cc_start: 0.7519 (m) cc_final: 0.6892 (p) REVERT: C 46 GLU cc_start: 0.7484 (tt0) cc_final: 0.6449 (tp30) REVERT: F 46 GLU cc_start: 0.7355 (tt0) cc_final: 0.7098 (tt0) REVERT: D 46 GLU cc_start: 0.7559 (tt0) cc_final: 0.6845 (tp30) REVERT: D 62 GLN cc_start: 0.7382 (tp40) cc_final: 0.6946 (tm-30) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.9813 time to fit residues: 52.5246 Evaluate side-chains 44 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 7.9990 chunk 11 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 8 optimal weight: 8.9990 chunk 35 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 3 optimal weight: 0.7980 overall best weight: 3.2586 ------------------------------------------------------------------------------- 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 = 0.4458 r_free = 0.4458 target = 0.161001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.116903 restraints weight = 2868.244| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 2.88 r_work: 0.3809 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2610 Z= 0.194 Angle : 0.524 3.762 3528 Z= 0.298 Chirality : 0.050 0.128 462 Planarity : 0.002 0.008 438 Dihedral : 4.638 14.434 378 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.31 % Favored : 81.69 % Rotamer: Outliers : 3.79 % Allowed : 14.77 % Favored : 81.44 % 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: -4.82 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.006 0.001 PHE E 94 TYR 0.012 0.003 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.02061 ( 19) hydrogen bonds : angle 4.08768 ( 57) covalent geometry : bond 0.00424 ( 2610) covalent geometry : angle 0.52413 ( 3528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.300 Fit side-chains REVERT: B 46 GLU cc_start: 0.7361 (tt0) cc_final: 0.6624 (tp30) REVERT: B 65 ASN cc_start: 0.7222 (t0) cc_final: 0.7008 (t0) REVERT: A 46 GLU cc_start: 0.7186 (tt0) cc_final: 0.6204 (tm-30) REVERT: E 43 LYS cc_start: 0.7774 (tttt) cc_final: 0.7397 (mtpm) REVERT: E 46 GLU cc_start: 0.7699 (tt0) cc_final: 0.6692 (tp30) REVERT: E 92 THR cc_start: 0.7587 (m) cc_final: 0.7106 (p) REVERT: C 46 GLU cc_start: 0.7533 (tt0) cc_final: 0.6823 (tp30) REVERT: F 46 GLU cc_start: 0.7411 (tt0) cc_final: 0.7171 (tt0) REVERT: F 92 THR cc_start: 0.7979 (m) cc_final: 0.7513 (p) REVERT: D 46 GLU cc_start: 0.7748 (tt0) cc_final: 0.7048 (tp30) REVERT: D 62 GLN cc_start: 0.7296 (tp40) cc_final: 0.7033 (tm-30) outliers start: 10 outliers final: 9 residues processed: 49 average time/residue: 1.0090 time to fit residues: 50.8920 Evaluate side-chains 45 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.3980 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 2 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 17 optimal weight: 20.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.161024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.117877 restraints weight = 2878.695| |-----------------------------------------------------------------------------| r_work (start): 0.3935 rms_B_bonded: 2.89 r_work: 0.3801 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3671 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2610 Z= 0.238 Angle : 0.584 4.168 3528 Z= 0.334 Chirality : 0.051 0.123 462 Planarity : 0.003 0.009 438 Dihedral : 5.092 14.531 378 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.04 % Favored : 78.96 % Rotamer: Outliers : 4.17 % Allowed : 14.77 % Favored : 81.06 % 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: -5.08 (0.31), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.87 (0.24), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.007 0.002 PHE E 94 TYR 0.014 0.004 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02307 ( 19) hydrogen bonds : angle 4.22864 ( 57) covalent geometry : bond 0.00514 ( 2610) covalent geometry : angle 0.58389 ( 3528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.301 Fit side-chains REVERT: B 46 GLU cc_start: 0.7496 (tt0) cc_final: 0.6713 (tp30) REVERT: B 65 ASN cc_start: 0.7436 (t0) cc_final: 0.7174 (t0) REVERT: A 46 GLU cc_start: 0.7362 (tt0) cc_final: 0.6349 (tm-30) REVERT: E 43 LYS cc_start: 0.7883 (tttt) cc_final: 0.7516 (mtpm) REVERT: E 46 GLU cc_start: 0.7888 (tt0) cc_final: 0.6788 (tp30) REVERT: E 92 THR cc_start: 0.7624 (m) cc_final: 0.7167 (p) REVERT: C 46 GLU cc_start: 0.7849 (tt0) cc_final: 0.6928 (tp30) REVERT: F 46 GLU cc_start: 0.7696 (tt0) cc_final: 0.7479 (tt0) REVERT: F 92 THR cc_start: 0.8034 (m) cc_final: 0.7632 (p) REVERT: D 43 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7907 (mtpp) REVERT: D 46 GLU cc_start: 0.7896 (tt0) cc_final: 0.7101 (tp30) REVERT: D 62 GLN cc_start: 0.7269 (tp40) cc_final: 0.6372 (tp40) outliers start: 11 outliers final: 9 residues processed: 52 average time/residue: 1.0088 time to fit residues: 53.9565 Evaluate side-chains 50 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 35 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 8.9990 chunk 13 optimal weight: 1.9990 chunk 11 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 10 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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 = 0.4505 r_free = 0.4505 target = 0.164435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.121062 restraints weight = 2863.549| |-----------------------------------------------------------------------------| r_work (start): 0.3994 rms_B_bonded: 2.89 r_work: 0.3859 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2610 Z= 0.120 Angle : 0.466 4.205 3528 Z= 0.260 Chirality : 0.049 0.126 462 Planarity : 0.002 0.005 438 Dihedral : 4.490 14.630 378 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.93 % Favored : 86.07 % Rotamer: Outliers : 3.79 % Allowed : 15.15 % Favored : 81.06 % 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: -4.73 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.004 0.001 PHE B 94 TYR 0.007 0.002 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.01436 ( 19) hydrogen bonds : angle 3.80206 ( 57) covalent geometry : bond 0.00257 ( 2610) covalent geometry : angle 0.46558 ( 3528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.272 Fit side-chains REVERT: B 46 GLU cc_start: 0.7351 (tt0) cc_final: 0.6593 (tp30) REVERT: B 65 ASN cc_start: 0.7242 (t0) cc_final: 0.6946 (t0) REVERT: A 46 GLU cc_start: 0.7182 (tt0) cc_final: 0.6166 (tm-30) REVERT: E 43 LYS cc_start: 0.7689 (tttt) cc_final: 0.7383 (mtpm) REVERT: E 46 GLU cc_start: 0.7614 (tt0) cc_final: 0.6590 (tp30) REVERT: E 92 THR cc_start: 0.7580 (m) cc_final: 0.7108 (p) REVERT: C 46 GLU cc_start: 0.7696 (tt0) cc_final: 0.6774 (tp30) REVERT: C 57 GLU cc_start: 0.7895 (tt0) cc_final: 0.7533 (tt0) REVERT: F 46 GLU cc_start: 0.7441 (tt0) cc_final: 0.7184 (tt0) REVERT: F 92 THR cc_start: 0.7939 (m) cc_final: 0.7533 (p) REVERT: D 46 GLU cc_start: 0.7570 (tt0) cc_final: 0.6961 (tp30) outliers start: 10 outliers final: 8 residues processed: 54 average time/residue: 1.0099 time to fit residues: 56.0696 Evaluate side-chains 47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 0.0970 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- 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 = 0.4461 r_free = 0.4461 target = 0.160415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.117189 restraints weight = 2921.983| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 2.92 r_work: 0.3819 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 2610 Z= 0.215 Angle : 0.564 4.677 3528 Z= 0.318 Chirality : 0.050 0.123 462 Planarity : 0.003 0.008 438 Dihedral : 4.892 15.541 378 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.22 % Favored : 79.78 % Rotamer: Outliers : 4.55 % Allowed : 15.91 % Favored : 79.55 % 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: -4.87 (0.32), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.70 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.007 0.002 PHE E 94 TYR 0.013 0.003 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.02022 ( 19) hydrogen bonds : angle 4.02072 ( 57) covalent geometry : bond 0.00468 ( 2610) covalent geometry : angle 0.56351 ( 3528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.325 Fit side-chains REVERT: B 46 GLU cc_start: 0.7327 (tt0) cc_final: 0.6646 (tp30) REVERT: B 65 ASN cc_start: 0.7267 (t0) cc_final: 0.6990 (t0) REVERT: A 46 GLU cc_start: 0.7261 (tt0) cc_final: 0.6306 (tm-30) REVERT: E 43 LYS cc_start: 0.7754 (tttt) cc_final: 0.7397 (mtpm) REVERT: E 46 GLU cc_start: 0.7754 (tt0) cc_final: 0.6872 (tm-30) REVERT: E 54 THR cc_start: 0.8600 (m) cc_final: 0.8384 (m) REVERT: E 92 THR cc_start: 0.7624 (m) cc_final: 0.7152 (p) REVERT: C 46 GLU cc_start: 0.7545 (tt0) cc_final: 0.6864 (tp30) REVERT: C 57 GLU cc_start: 0.7896 (tt0) cc_final: 0.7531 (tt0) REVERT: F 46 GLU cc_start: 0.7475 (tt0) cc_final: 0.7243 (tt0) REVERT: F 92 THR cc_start: 0.7954 (m) cc_final: 0.7557 (p) REVERT: D 43 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7827 (mtpp) REVERT: D 46 GLU cc_start: 0.7675 (tt0) cc_final: 0.7036 (tp30) outliers start: 12 outliers final: 10 residues processed: 50 average time/residue: 1.2306 time to fit residues: 63.5537 Evaluate side-chains 47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 36 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 43 LYS Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 8.9990 chunk 26 optimal weight: 10.0000 chunk 34 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- 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 = 0.4508 r_free = 0.4508 target = 0.164000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.120767 restraints weight = 2831.688| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.89 r_work: 0.3862 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2610 Z= 0.129 Angle : 0.482 4.841 3528 Z= 0.267 Chirality : 0.049 0.125 462 Planarity : 0.002 0.005 438 Dihedral : 4.488 14.559 378 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.21 % Favored : 85.79 % Rotamer: Outliers : 4.55 % Allowed : 16.67 % Favored : 78.79 % 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: -4.62 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.51 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.004 0.001 PHE E 94 TYR 0.007 0.002 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.01441 ( 19) hydrogen bonds : angle 3.73982 ( 57) covalent geometry : bond 0.00280 ( 2610) covalent geometry : angle 0.48226 ( 3528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 40 time to evaluate : 0.295 Fit side-chains REVERT: B 46 GLU cc_start: 0.7351 (tt0) cc_final: 0.6647 (tp30) REVERT: B 65 ASN cc_start: 0.7258 (t0) cc_final: 0.6958 (t0) REVERT: A 46 GLU cc_start: 0.7183 (tt0) cc_final: 0.6167 (tm-30) REVERT: E 43 LYS cc_start: 0.7684 (tttt) cc_final: 0.7418 (mtpm) REVERT: E 46 GLU cc_start: 0.7626 (tt0) cc_final: 0.6618 (tp30) REVERT: E 59 THR cc_start: 0.6716 (OUTLIER) cc_final: 0.6513 (m) REVERT: E 92 THR cc_start: 0.7565 (m) cc_final: 0.7101 (p) REVERT: C 46 GLU cc_start: 0.7610 (tt0) cc_final: 0.6672 (tp30) REVERT: C 57 GLU cc_start: 0.7835 (tt0) cc_final: 0.7342 (tt0) REVERT: F 46 GLU cc_start: 0.7398 (tt0) cc_final: 0.7151 (tt0) REVERT: F 92 THR cc_start: 0.7934 (m) cc_final: 0.7540 (p) REVERT: D 46 GLU cc_start: 0.7567 (tt0) cc_final: 0.6961 (tp30) outliers start: 12 outliers final: 9 residues processed: 52 average time/residue: 0.9498 time to fit residues: 50.8941 Evaluate side-chains 47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 59 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 32 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 13 optimal weight: 8.9990 chunk 29 optimal weight: 0.0470 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 0.0050 chunk 10 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 overall best weight: 3.4098 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.160548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.117488 restraints weight = 2888.111| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.90 r_work: 0.3828 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2610 Z= 0.205 Angle : 0.561 5.137 3528 Z= 0.313 Chirality : 0.050 0.124 462 Planarity : 0.003 0.007 438 Dihedral : 4.798 15.606 378 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.22 % Favored : 79.78 % Rotamer: Outliers : 3.79 % Allowed : 16.67 % Favored : 79.55 % 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: -4.79 (0.33), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.25), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 50 PHE 0.006 0.001 PHE E 94 TYR 0.013 0.003 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.01909 ( 19) hydrogen bonds : angle 3.92917 ( 57) covalent geometry : bond 0.00448 ( 2610) covalent geometry : angle 0.56067 ( 3528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.305 Fit side-chains REVERT: B 46 GLU cc_start: 0.7314 (tt0) cc_final: 0.6633 (tp30) REVERT: B 65 ASN cc_start: 0.7251 (t0) cc_final: 0.6964 (t0) REVERT: A 46 GLU cc_start: 0.7188 (tt0) cc_final: 0.6217 (tm-30) REVERT: E 43 LYS cc_start: 0.7748 (tttt) cc_final: 0.7390 (mtpm) REVERT: E 46 GLU cc_start: 0.7716 (tt0) cc_final: 0.6845 (tm-30) REVERT: E 92 THR cc_start: 0.7590 (m) cc_final: 0.7128 (p) REVERT: C 46 GLU cc_start: 0.7529 (tt0) cc_final: 0.6835 (tp30) REVERT: C 57 GLU cc_start: 0.7885 (tt0) cc_final: 0.7500 (tt0) REVERT: F 46 GLU cc_start: 0.7462 (tt0) cc_final: 0.7230 (tt0) REVERT: F 92 THR cc_start: 0.7939 (m) cc_final: 0.7549 (p) REVERT: D 46 GLU cc_start: 0.7725 (tt0) cc_final: 0.7047 (tp30) outliers start: 10 outliers final: 8 residues processed: 49 average time/residue: 0.9715 time to fit residues: 49.1180 Evaluate side-chains 47 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.0060 chunk 14 optimal weight: 6.9990 chunk 27 optimal weight: 0.0970 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.167463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.124102 restraints weight = 2756.916| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 2.86 r_work: 0.3904 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2610 Z= 0.097 Angle : 0.470 5.669 3528 Z= 0.254 Chirality : 0.049 0.124 462 Planarity : 0.001 0.004 438 Dihedral : 4.221 13.280 378 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.20 % Favored : 88.80 % Rotamer: Outliers : 2.65 % Allowed : 17.42 % Favored : 79.92 % 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: -4.45 (0.35), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.004 0.001 PHE A 94 TYR 0.005 0.001 TYR B 39 Details of bonding type rmsd hydrogen bonds : bond 0.01103 ( 19) hydrogen bonds : angle 3.49850 ( 57) covalent geometry : bond 0.00213 ( 2610) covalent geometry : angle 0.46967 ( 3528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.277 Fit side-chains REVERT: B 46 GLU cc_start: 0.7380 (tt0) cc_final: 0.6643 (tp30) REVERT: A 46 GLU cc_start: 0.7195 (tt0) cc_final: 0.6091 (tm-30) REVERT: E 43 LYS cc_start: 0.7679 (tttt) cc_final: 0.7408 (mtpm) REVERT: E 46 GLU cc_start: 0.7723 (tt0) cc_final: 0.7322 (tt0) REVERT: E 92 THR cc_start: 0.7527 (m) cc_final: 0.6943 (p) REVERT: C 46 GLU cc_start: 0.7615 (tt0) cc_final: 0.6665 (tp30) REVERT: C 57 GLU cc_start: 0.7836 (tt0) cc_final: 0.7324 (tt0) REVERT: F 46 GLU cc_start: 0.7421 (tt0) cc_final: 0.7166 (tt0) REVERT: F 92 THR cc_start: 0.7920 (m) cc_final: 0.7520 (p) REVERT: D 46 GLU cc_start: 0.7522 (tt0) cc_final: 0.6933 (tp30) outliers start: 7 outliers final: 5 residues processed: 47 average time/residue: 0.8706 time to fit residues: 42.2854 Evaluate side-chains 41 residues out of total 264 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain D residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 0.0170 chunk 26 optimal weight: 0.0170 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 21 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 0 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 1.2060 ------------------------------------------------------------------------------- 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 = 0.4549 r_free = 0.4549 target = 0.167454 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.123546 restraints weight = 2817.723| |-----------------------------------------------------------------------------| r_work (start): 0.4046 rms_B_bonded: 2.88 r_work: 0.3906 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2610 Z= 0.101 Angle : 0.482 5.642 3528 Z= 0.258 Chirality : 0.049 0.123 462 Planarity : 0.001 0.006 438 Dihedral : 4.042 12.401 378 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer: Outliers : 1.89 % Allowed : 19.32 % Favored : 78.79 % 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: -4.26 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.27), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.004 0.001 PHE A 94 TYR 0.006 0.001 TYR D 39 Details of bonding type rmsd hydrogen bonds : bond 0.01018 ( 19) hydrogen bonds : angle 3.37233 ( 57) covalent geometry : bond 0.00227 ( 2610) covalent geometry : angle 0.48210 ( 3528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2233.29 seconds wall clock time: 38 minutes 55.95 seconds (2335.95 seconds total)