Starting phenix.real_space_refine on Fri Aug 22 15:02:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vic_65083/08_2025/9vic_65083.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vic_65083/08_2025/9vic_65083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9vic_65083/08_2025/9vic_65083.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vic_65083/08_2025/9vic_65083.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vic_65083/08_2025/9vic_65083.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vic_65083/08_2025/9vic_65083.map" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.092 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Fe 4 7.16 5 S 12 5.16 5 C 2906 2.51 5 N 766 2.21 5 O 798 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4486 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1069 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 133} Chain: "B" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1084 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CMO': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {'CMO': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: C, D Time building chain proxies: 1.21, per 1000 atoms: 0.27 Number of scatterers: 4486 At special positions: 0 Unit cell: (70.38, 84.66, 66.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 4 26.01 S 12 16.00 O 798 8.00 N 766 7.00 C 2906 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 183.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1052 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 84.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 3 through 18 Processing helix chain 'A' and resid 20 through 36 Processing helix chain 'A' and resid 37 through 43 removed outlier: 3.641A pdb=" N TYR A 42 " --> pdb=" O THR A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 72 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 80 through 89 Processing helix chain 'A' and resid 95 through 113 removed outlier: 3.902A pdb=" N LYS A 99 " --> pdb=" O PRO A 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 100 " --> pdb=" O VAL A 96 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'B' and resid 4 through 16 Processing helix chain 'B' and resid 22 through 35 Processing helix chain 'B' and resid 36 through 46 removed outlier: 4.225A pdb=" N GLU B 43 " --> pdb=" O ARG B 40 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER B 44 " --> pdb=" O PHE B 41 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY B 46 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 57 Processing helix chain 'B' and resid 57 through 77 removed outlier: 3.504A pdb=" N LYS B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 Processing helix chain 'B' and resid 85 through 92 Processing helix chain 'B' and resid 100 through 119 removed outlier: 3.820A pdb=" N ARG B 104 " --> pdb=" O PRO B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 122 No H-bonds generated for 'chain 'B' and resid 120 through 122' Processing helix chain 'B' and resid 123 through 141 Processing helix chain 'C' and resid 3 through 18 Processing helix chain 'C' and resid 20 through 36 Processing helix chain 'C' and resid 37 through 43 removed outlier: 3.641A pdb=" N TYR C 42 " --> pdb=" O THR C 39 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 72 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 95 through 113 removed outlier: 3.902A pdb=" N LYS C 99 " --> pdb=" O PRO C 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 100 " --> pdb=" O VAL C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 138 Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 22 through 35 Processing helix chain 'D' and resid 36 through 46 removed outlier: 4.225A pdb=" N GLU D 43 " --> pdb=" O ARG D 40 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N SER D 44 " --> pdb=" O PHE D 41 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLY D 46 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 57 Processing helix chain 'D' and resid 57 through 77 removed outlier: 3.504A pdb=" N LYS D 61 " --> pdb=" O ASN D 57 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LYS D 66 " --> pdb=" O ALA D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 92 Processing helix chain 'D' and resid 100 through 119 removed outlier: 3.820A pdb=" N ARG D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 122 No H-bonds generated for 'chain 'D' and resid 120 through 122' Processing helix chain 'D' and resid 123 through 141 324 hydrogen bonds defined for protein. 924 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: 0.54 Time building geometry restraints manager: 0.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.39: 1826 1.39 - 1.57: 2762 1.57 - 1.76: 0 1.76 - 1.94: 22 1.94 - 2.13: 12 Bond restraints: 4622 Sorted by residual: bond pdb=" C3B HEM A 201 " pdb=" CAB HEM A 201 " ideal model delta sigma weight residual 1.544 1.442 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C3B HEM C 201 " pdb=" CAB HEM C 201 " ideal model delta sigma weight residual 1.544 1.442 0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" C1A HEM A 201 " pdb=" C2A HEM A 201 " ideal model delta sigma weight residual 1.449 1.352 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C1A HEM C 201 " pdb=" C2A HEM C 201 " ideal model delta sigma weight residual 1.449 1.352 0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" C3A HEM C 201 " pdb=" C4A HEM C 201 " ideal model delta sigma weight residual 1.449 1.361 0.088 2.00e-02 2.50e+03 1.94e+01 ... (remaining 4617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 5904 3.18 - 6.37: 392 6.37 - 9.55: 38 9.55 - 12.73: 2 12.73 - 15.91: 2 Bond angle restraints: 6338 Sorted by residual: angle pdb=" N TYR C 42 " pdb=" CA TYR C 42 " pdb=" CB TYR C 42 " ideal model delta sigma weight residual 110.46 94.55 15.91 1.57e+00 4.06e-01 1.03e+02 angle pdb=" N TYR A 42 " pdb=" CA TYR A 42 " pdb=" CB TYR A 42 " ideal model delta sigma weight residual 110.46 94.55 15.91 1.57e+00 4.06e-01 1.03e+02 angle pdb=" CA ASP A 94 " pdb=" CB ASP A 94 " pdb=" CG ASP A 94 " ideal model delta sigma weight residual 112.60 120.93 -8.33 1.00e+00 1.00e+00 6.94e+01 angle pdb=" CA ASP C 94 " pdb=" CB ASP C 94 " pdb=" CG ASP C 94 " ideal model delta sigma weight residual 112.60 120.93 -8.33 1.00e+00 1.00e+00 6.94e+01 angle pdb=" CA PHE C 43 " pdb=" CB PHE C 43 " pdb=" CG PHE C 43 " ideal model delta sigma weight residual 113.80 120.77 -6.97 1.00e+00 1.00e+00 4.86e+01 ... (remaining 6333 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2344 17.88 - 35.75: 194 35.75 - 53.62: 58 53.62 - 71.50: 16 71.50 - 89.37: 10 Dihedral angle restraints: 2622 sinusoidal: 998 harmonic: 1624 Sorted by residual: dihedral pdb=" N TYR C 42 " pdb=" C TYR C 42 " pdb=" CA TYR C 42 " pdb=" CB TYR C 42 " ideal model delta harmonic sigma weight residual 122.80 106.32 16.48 0 2.50e+00 1.60e-01 4.35e+01 dihedral pdb=" N TYR A 42 " pdb=" C TYR A 42 " pdb=" CA TYR A 42 " pdb=" CB TYR A 42 " ideal model delta harmonic sigma weight residual 122.80 106.32 16.48 0 2.50e+00 1.60e-01 4.35e+01 dihedral pdb=" CD ARG C 92 " pdb=" NE ARG C 92 " pdb=" CZ ARG C 92 " pdb=" NH1 ARG C 92 " ideal model delta sinusoidal sigma weight residual 0.00 52.70 -52.70 1 1.00e+01 1.00e-02 3.78e+01 ... (remaining 2619 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.064: 412 0.064 - 0.128: 172 0.128 - 0.191: 66 0.191 - 0.254: 30 0.254 - 0.318: 10 Chirality restraints: 690 Sorted by residual: chirality pdb=" CA TYR A 140 " pdb=" N TYR A 140 " pdb=" C TYR A 140 " pdb=" CB TYR A 140 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA TYR C 140 " pdb=" N TYR C 140 " pdb=" C TYR C 140 " pdb=" CB TYR C 140 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" CA PRO B 124 " pdb=" N PRO B 124 " pdb=" C PRO B 124 " pdb=" CB PRO B 124 " both_signs ideal model delta sigma weight residual False 2.72 2.41 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 687 not shown) Planarity restraints: 792 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG C 92 " -0.931 9.50e-02 1.11e+02 4.18e-01 1.12e+02 pdb=" NE ARG C 92 " 0.043 2.00e-02 2.50e+03 pdb=" CZ ARG C 92 " 0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG C 92 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG C 92 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 92 " 0.931 9.50e-02 1.11e+02 4.18e-01 1.12e+02 pdb=" NE ARG A 92 " -0.043 2.00e-02 2.50e+03 pdb=" CZ ARG A 92 " -0.053 2.00e-02 2.50e+03 pdb=" NH1 ARG A 92 " 0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG A 92 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 141 " 0.838 9.50e-02 1.11e+02 3.77e-01 9.80e+01 pdb=" NE ARG A 141 " -0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 141 " -0.070 2.00e-02 2.50e+03 pdb=" NH1 ARG A 141 " 0.018 2.00e-02 2.50e+03 pdb=" NH2 ARG A 141 " 0.044 2.00e-02 2.50e+03 ... (remaining 789 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.83: 1112 2.83 - 3.59: 7052 3.59 - 4.34: 13492 4.34 - 5.10: 22584 5.10 - 5.86: 26572 Nonbonded interactions: 70812 Sorted by model distance: nonbonded pdb=" O VAL C 93 " pdb=" OH TYR C 140 " model vdw 2.069 3.040 nonbonded pdb=" O VAL A 93 " pdb=" OH TYR A 140 " model vdw 2.069 3.040 nonbonded pdb=" O SER A 138 " pdb=" OG SER A 138 " model vdw 2.295 3.040 nonbonded pdb=" O SER C 138 " pdb=" OG SER C 138 " model vdw 2.295 3.040 nonbonded pdb=" O PRO C 114 " pdb=" NE2 HIS D 116 " model vdw 2.471 3.120 ... (remaining 70807 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.016 0.313 4626 Z= 0.781 Angle : 1.763 15.913 6338 Z= 1.150 Chirality : 0.092 0.318 690 Planarity : 0.031 0.418 792 Dihedral : 16.508 89.374 1570 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 1.08 % Allowed : 1.43 % Favored : 97.49 % Rotamer: Outliers : 3.96 % Allowed : 6.17 % Favored : 89.87 % Cbeta Deviations : 1.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.50 (0.28), residues: 558 helix: -1.55 (0.20), residues: 440 sheet: None (None), residues: 0 loop : -1.20 (0.49), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.060 0.013 ARG A 141 TYR 0.050 0.018 TYR C 24 PHE 0.051 0.011 PHE C 98 TRP 0.037 0.013 TRP B 37 HIS 0.032 0.006 HIS A 87 Details of bonding type rmsd covalent geometry : bond 0.01402 ( 4622) covalent geometry : angle 1.76257 ( 6338) hydrogen bonds : bond 0.21393 ( 324) hydrogen bonds : angle 6.83103 ( 924) Misc. bond : bond 0.23079 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 110 time to evaluate : 0.164 Fit side-chains REVERT: A 81 SER cc_start: 0.8038 (p) cc_final: 0.7724 (t) REVERT: A 85 ASP cc_start: 0.7845 (t70) cc_final: 0.7306 (m-30) REVERT: A 99 LYS cc_start: 0.8479 (mttm) cc_final: 0.8147 (mttt) REVERT: B 3 LEU cc_start: 0.5898 (OUTLIER) cc_final: 0.5657 (mt) REVERT: B 26 GLU cc_start: 0.8021 (tp30) cc_final: 0.7125 (mt-10) REVERT: B 43 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7281 (pm20) REVERT: B 61 LYS cc_start: 0.8189 (tttt) cc_final: 0.7367 (mttp) REVERT: B 66 LYS cc_start: 0.8001 (mtpt) cc_final: 0.7488 (mtmm) REVERT: B 73 ASP cc_start: 0.7400 (t0) cc_final: 0.6561 (m-30) REVERT: B 101 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.7983 (tp30) REVERT: B 139 ASN cc_start: 0.7911 (t0) cc_final: 0.7670 (t0) REVERT: C 81 SER cc_start: 0.8040 (p) cc_final: 0.7725 (t) REVERT: C 85 ASP cc_start: 0.7847 (t70) cc_final: 0.7308 (m-30) REVERT: C 99 LYS cc_start: 0.8479 (mttm) cc_final: 0.8148 (mttt) REVERT: D 3 LEU cc_start: 0.5894 (OUTLIER) cc_final: 0.5654 (mt) REVERT: D 26 GLU cc_start: 0.8021 (tp30) cc_final: 0.7122 (mt-10) REVERT: D 43 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7280 (pm20) REVERT: D 61 LYS cc_start: 0.8187 (tttt) cc_final: 0.7366 (mttp) REVERT: D 66 LYS cc_start: 0.8003 (mtpt) cc_final: 0.7488 (mtmm) REVERT: D 73 ASP cc_start: 0.7398 (t0) cc_final: 0.6561 (m-30) REVERT: D 101 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7980 (tp30) REVERT: D 139 ASN cc_start: 0.7914 (t0) cc_final: 0.7673 (t0) outliers start: 18 outliers final: 0 residues processed: 120 average time/residue: 0.5043 time to fit residues: 62.5805 Evaluate side-chains 106 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 54 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS A 89 HIS B 63 HIS B 131 GLN C 58 HIS C 89 HIS D 63 HIS D 131 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.144542 restraints weight = 4402.974| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.19 r_work: 0.3509 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 4626 Z= 0.139 Angle : 0.663 5.781 6338 Z= 0.317 Chirality : 0.040 0.126 690 Planarity : 0.006 0.047 792 Dihedral : 12.827 86.196 634 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.57 % Rotamer: Outliers : 4.85 % Allowed : 9.69 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.82 (0.35), residues: 558 helix: 1.46 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 0.59 (0.57), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 141 TYR 0.012 0.002 TYR C 42 PHE 0.010 0.001 PHE D 42 TRP 0.014 0.002 TRP C 14 HIS 0.003 0.001 HIS C 112 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 4622) covalent geometry : angle 0.66252 ( 6338) hydrogen bonds : bond 0.03998 ( 324) hydrogen bonds : angle 3.80778 ( 924) Misc. bond : bond 0.07005 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.173 Fit side-chains REVERT: A 27 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8584 (tt0) REVERT: A 99 LYS cc_start: 0.8728 (mttm) cc_final: 0.8503 (mttt) REVERT: B 3 LEU cc_start: 0.6909 (mp) cc_final: 0.6641 (mp) REVERT: B 43 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: B 55 MET cc_start: 0.8295 (mmm) cc_final: 0.7966 (mmm) REVERT: B 61 LYS cc_start: 0.8289 (tttt) cc_final: 0.7880 (mttp) REVERT: B 101 GLU cc_start: 0.7955 (OUTLIER) cc_final: 0.7398 (tm-30) REVERT: C 27 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8568 (tt0) REVERT: C 99 LYS cc_start: 0.8714 (mttm) cc_final: 0.8491 (mttt) REVERT: D 3 LEU cc_start: 0.6891 (mp) cc_final: 0.6623 (mp) REVERT: D 43 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7639 (pm20) REVERT: D 55 MET cc_start: 0.8296 (mmm) cc_final: 0.7965 (mmm) REVERT: D 61 LYS cc_start: 0.8283 (tttt) cc_final: 0.7887 (mttp) REVERT: D 101 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7412 (tm-30) outliers start: 22 outliers final: 4 residues processed: 108 average time/residue: 0.5728 time to fit residues: 63.7680 Evaluate side-chains 104 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 48 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 57 ASN D 39 GLN D 57 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.141983 restraints weight = 4241.913| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 1.17 r_work: 0.3496 rms_B_bonded: 1.79 restraints_weight: 0.5000 r_work: 0.3397 rms_B_bonded: 3.04 restraints_weight: 0.2500 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.2282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4626 Z= 0.146 Angle : 0.638 5.894 6338 Z= 0.304 Chirality : 0.040 0.125 690 Planarity : 0.007 0.049 792 Dihedral : 11.964 88.633 630 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 3.96 % Allowed : 17.62 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.79 (0.36), residues: 558 helix: 2.20 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 0.76 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 92 TYR 0.009 0.002 TYR C 42 PHE 0.011 0.002 PHE D 42 TRP 0.012 0.002 TRP A 14 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 4622) covalent geometry : angle 0.63826 ( 6338) hydrogen bonds : bond 0.04128 ( 324) hydrogen bonds : angle 3.69484 ( 924) Misc. bond : bond 0.03448 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.180 Fit side-chains REVERT: A 27 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8554 (tt0) REVERT: A 85 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7374 (t70) REVERT: B 43 GLU cc_start: 0.7921 (OUTLIER) cc_final: 0.7602 (pm20) REVERT: B 55 MET cc_start: 0.8417 (mmm) cc_final: 0.8067 (mmm) REVERT: B 61 LYS cc_start: 0.8284 (tttt) cc_final: 0.7899 (mttp) REVERT: B 101 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7327 (tm-30) REVERT: C 27 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: C 85 ASP cc_start: 0.7617 (OUTLIER) cc_final: 0.7386 (t70) REVERT: D 43 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7622 (pm20) REVERT: D 55 MET cc_start: 0.8428 (mmm) cc_final: 0.8075 (mmm) REVERT: D 61 LYS cc_start: 0.8274 (tttt) cc_final: 0.7897 (mttp) REVERT: D 101 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7300 (tm-30) outliers start: 18 outliers final: 6 residues processed: 92 average time/residue: 0.5320 time to fit residues: 50.6368 Evaluate side-chains 100 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 19 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 40 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.161127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.142676 restraints weight = 4335.402| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.15 r_work: 0.3475 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 4626 Z= 0.164 Angle : 0.653 5.857 6338 Z= 0.311 Chirality : 0.042 0.130 690 Planarity : 0.007 0.045 792 Dihedral : 11.658 82.986 630 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 6.17 % Allowed : 17.62 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.92 (0.36), residues: 558 helix: 2.29 (0.24), residues: 430 sheet: None (None), residues: 0 loop : 0.86 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 92 TYR 0.008 0.002 TYR C 42 PHE 0.013 0.002 PHE B 42 TRP 0.010 0.002 TRP A 14 HIS 0.006 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 4622) covalent geometry : angle 0.65286 ( 6338) hydrogen bonds : bond 0.04360 ( 324) hydrogen bonds : angle 3.74148 ( 924) Misc. bond : bond 0.02870 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 84 time to evaluate : 0.112 Fit side-chains REVERT: A 85 ASP cc_start: 0.7670 (OUTLIER) cc_final: 0.7466 (t70) REVERT: A 139 LYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6213 (mttt) REVERT: B 3 LEU cc_start: 0.7086 (OUTLIER) cc_final: 0.6720 (mt) REVERT: B 43 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7620 (pm20) REVERT: B 55 MET cc_start: 0.8401 (mmm) cc_final: 0.8020 (mmm) REVERT: B 61 LYS cc_start: 0.8366 (tttt) cc_final: 0.7898 (mttp) REVERT: B 101 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7343 (tm-30) REVERT: C 85 ASP cc_start: 0.7674 (OUTLIER) cc_final: 0.7470 (t70) REVERT: C 139 LYS cc_start: 0.7025 (OUTLIER) cc_final: 0.6218 (mttt) REVERT: D 3 LEU cc_start: 0.7089 (OUTLIER) cc_final: 0.6723 (mt) REVERT: D 43 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7642 (pm20) REVERT: D 55 MET cc_start: 0.8409 (mmm) cc_final: 0.8023 (mmm) REVERT: D 61 LYS cc_start: 0.8379 (tttt) cc_final: 0.7921 (mttp) REVERT: D 101 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7333 (tm-30) outliers start: 28 outliers final: 8 residues processed: 98 average time/residue: 0.5637 time to fit residues: 56.9664 Evaluate side-chains 102 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain C residue 139 LYS Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 96 LEU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 11 optimal weight: 1.9990 chunk 52 optimal weight: 0.0970 chunk 4 optimal weight: 0.0470 chunk 17 optimal weight: 0.0970 chunk 25 optimal weight: 1.9990 chunk 49 optimal weight: 0.0270 chunk 46 optimal weight: 0.3980 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.6980 overall best weight: 0.1332 ------------------------------------------------------------------------------- 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 = 0.3891 r_free = 0.3891 target = 0.168122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.149406 restraints weight = 4252.037| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 1.18 r_work: 0.3581 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3478 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 4626 Z= 0.095 Angle : 0.549 6.481 6338 Z= 0.246 Chirality : 0.035 0.111 690 Planarity : 0.006 0.043 792 Dihedral : 10.668 82.126 630 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.57 % Rotamer: Outliers : 4.85 % Allowed : 18.50 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.07 (0.36), residues: 558 helix: 3.08 (0.25), residues: 428 sheet: None (None), residues: 0 loop : 1.38 (0.58), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 92 TYR 0.007 0.001 TYR C 140 PHE 0.005 0.001 PHE B 42 TRP 0.008 0.001 TRP C 14 HIS 0.003 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 4622) covalent geometry : angle 0.54900 ( 6338) hydrogen bonds : bond 0.02264 ( 324) hydrogen bonds : angle 3.41243 ( 924) Misc. bond : bond 0.08767 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.170 Fit side-chains REVERT: B 3 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6791 (mp) REVERT: B 8 LYS cc_start: 0.7369 (mttm) cc_final: 0.7077 (mttt) REVERT: B 43 GLU cc_start: 0.7781 (OUTLIER) cc_final: 0.7480 (pm20) REVERT: B 55 MET cc_start: 0.8339 (mmm) cc_final: 0.8038 (mmm) REVERT: B 61 LYS cc_start: 0.8084 (tttt) cc_final: 0.7798 (mttp) REVERT: B 101 GLU cc_start: 0.7730 (OUTLIER) cc_final: 0.7234 (tm-30) REVERT: B 104 ARG cc_start: 0.8008 (ttt-90) cc_final: 0.7757 (mtt90) REVERT: D 3 LEU cc_start: 0.7092 (OUTLIER) cc_final: 0.6791 (mp) REVERT: D 8 LYS cc_start: 0.7352 (mttm) cc_final: 0.7057 (mttt) REVERT: D 43 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7473 (pm20) REVERT: D 55 MET cc_start: 0.8323 (mmm) cc_final: 0.8018 (mmm) REVERT: D 61 LYS cc_start: 0.8094 (tttt) cc_final: 0.7807 (mttp) REVERT: D 101 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7247 (tm-30) REVERT: D 104 ARG cc_start: 0.7985 (ttt-90) cc_final: 0.7746 (mtt90) outliers start: 22 outliers final: 2 residues processed: 98 average time/residue: 0.6029 time to fit residues: 60.9702 Evaluate side-chains 92 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 84 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 0.6980 chunk 44 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 GLN B 117 HIS D 39 GLN D 117 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.163841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.144916 restraints weight = 4405.624| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 1.19 r_work: 0.3505 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4626 Z= 0.125 Angle : 0.609 8.279 6338 Z= 0.278 Chirality : 0.039 0.125 690 Planarity : 0.006 0.043 792 Dihedral : 10.920 80.137 630 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 3.96 % Allowed : 20.26 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.87 (0.36), residues: 558 helix: 2.95 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.26 (0.59), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 141 TYR 0.006 0.002 TYR D 130 PHE 0.010 0.001 PHE D 42 TRP 0.009 0.001 TRP C 14 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 4622) covalent geometry : angle 0.60934 ( 6338) hydrogen bonds : bond 0.03459 ( 324) hydrogen bonds : angle 3.52041 ( 924) Misc. bond : bond 0.01378 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.123 Fit side-chains REVERT: B 3 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6760 (mp) REVERT: B 43 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7577 (pm20) REVERT: B 55 MET cc_start: 0.8352 (mmm) cc_final: 0.8107 (mmm) REVERT: B 61 LYS cc_start: 0.8243 (tttt) cc_final: 0.7862 (mttp) REVERT: B 90 GLU cc_start: 0.7249 (OUTLIER) cc_final: 0.6856 (mt-10) REVERT: B 101 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7309 (tm-30) REVERT: D 3 LEU cc_start: 0.7056 (OUTLIER) cc_final: 0.6743 (mp) REVERT: D 43 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7588 (pm20) REVERT: D 55 MET cc_start: 0.8347 (mmm) cc_final: 0.8101 (mmm) REVERT: D 61 LYS cc_start: 0.8241 (tttt) cc_final: 0.7854 (mttp) REVERT: D 90 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6826 (mt-10) REVERT: D 101 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7308 (tm-30) outliers start: 18 outliers final: 8 residues processed: 94 average time/residue: 0.4874 time to fit residues: 47.4867 Evaluate side-chains 104 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 90 GLU Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 38 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS D 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.163410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.144493 restraints weight = 4359.300| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.18 r_work: 0.3499 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.08 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4626 Z= 0.131 Angle : 0.616 7.574 6338 Z= 0.283 Chirality : 0.039 0.127 690 Planarity : 0.006 0.044 792 Dihedral : 10.981 81.302 630 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 4.85 % Allowed : 18.94 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.36), residues: 558 helix: 2.87 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.16 (0.58), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 141 TYR 0.007 0.002 TYR B 130 PHE 0.010 0.001 PHE B 42 TRP 0.008 0.001 TRP A 14 HIS 0.005 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4622) covalent geometry : angle 0.61574 ( 6338) hydrogen bonds : bond 0.03618 ( 324) hydrogen bonds : angle 3.56483 ( 924) Misc. bond : bond 0.00384 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.107 Fit side-chains REVERT: A 85 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7366 (t70) REVERT: B 3 LEU cc_start: 0.7047 (OUTLIER) cc_final: 0.6733 (mp) REVERT: B 43 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7518 (pm20) REVERT: B 55 MET cc_start: 0.8389 (mmm) cc_final: 0.8015 (mmm) REVERT: B 61 LYS cc_start: 0.8258 (tttt) cc_final: 0.7843 (mttp) REVERT: B 101 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7288 (tm-30) REVERT: C 85 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.7373 (t70) REVERT: D 3 LEU cc_start: 0.7038 (OUTLIER) cc_final: 0.6724 (mp) REVERT: D 43 GLU cc_start: 0.7822 (OUTLIER) cc_final: 0.7546 (pm20) REVERT: D 55 MET cc_start: 0.8398 (mmm) cc_final: 0.8022 (mmm) REVERT: D 61 LYS cc_start: 0.8242 (tttt) cc_final: 0.7823 (mttp) REVERT: D 90 GLU cc_start: 0.7277 (OUTLIER) cc_final: 0.7073 (mt-10) REVERT: D 101 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7306 (tm-30) outliers start: 22 outliers final: 8 residues processed: 94 average time/residue: 0.4722 time to fit residues: 46.0222 Evaluate side-chains 105 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 85 ASP Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 85 ASP Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 6.9990 chunk 2 optimal weight: 0.0980 chunk 52 optimal weight: 0.9990 chunk 30 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 25 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.0770 overall best weight: 0.3738 ------------------------------------------------------------------------------- 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 = 0.3864 r_free = 0.3864 target = 0.166504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.147898 restraints weight = 4364.545| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.18 r_work: 0.3541 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3443 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4626 Z= 0.102 Angle : 0.568 7.115 6338 Z= 0.256 Chirality : 0.037 0.119 690 Planarity : 0.005 0.043 792 Dihedral : 10.617 81.595 630 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.57 % Rotamer: Outliers : 4.19 % Allowed : 19.60 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.19 (0.36), residues: 558 helix: 3.15 (0.25), residues: 428 sheet: None (None), residues: 0 loop : 1.52 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.006 0.001 TYR B 130 PHE 0.007 0.001 PHE D 42 TRP 0.007 0.001 TRP A 14 HIS 0.004 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 4622) covalent geometry : angle 0.56825 ( 6338) hydrogen bonds : bond 0.02740 ( 324) hydrogen bonds : angle 3.42722 ( 924) Misc. bond : bond 0.03529 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.175 Fit side-chains REVERT: B 3 LEU cc_start: 0.7081 (OUTLIER) cc_final: 0.6795 (mp) REVERT: B 43 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7506 (pm20) REVERT: B 55 MET cc_start: 0.8319 (mmm) cc_final: 0.8030 (mmm) REVERT: B 61 LYS cc_start: 0.8145 (tttt) cc_final: 0.7815 (mttp) REVERT: B 101 GLU cc_start: 0.7746 (OUTLIER) cc_final: 0.7245 (tm-30) REVERT: D 3 LEU cc_start: 0.7066 (OUTLIER) cc_final: 0.6781 (mp) REVERT: D 43 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7519 (pm20) REVERT: D 55 MET cc_start: 0.8312 (mmm) cc_final: 0.8018 (mmm) REVERT: D 61 LYS cc_start: 0.8140 (tttt) cc_final: 0.7812 (mttp) REVERT: D 90 GLU cc_start: 0.7228 (OUTLIER) cc_final: 0.6825 (mt-10) REVERT: D 101 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7262 (tm-30) outliers start: 19 outliers final: 6 residues processed: 93 average time/residue: 0.4825 time to fit residues: 46.5808 Evaluate side-chains 94 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 43 GLU Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 43 GLU Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 1.9990 chunk 40 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.0370 chunk 32 optimal weight: 0.4980 chunk 11 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 117 HIS D 117 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.146627 restraints weight = 4359.276| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.19 r_work: 0.3529 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4626 Z= 0.110 Angle : 0.581 6.910 6338 Z= 0.264 Chirality : 0.038 0.124 690 Planarity : 0.006 0.043 792 Dihedral : 10.622 80.993 630 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 3.74 % Allowed : 20.48 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 4.15 (0.36), residues: 558 helix: 3.13 (0.25), residues: 428 sheet: None (None), residues: 0 loop : 1.47 (0.59), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 141 TYR 0.006 0.001 TYR D 130 PHE 0.008 0.001 PHE D 42 TRP 0.007 0.001 TRP C 14 HIS 0.005 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 4622) covalent geometry : angle 0.58110 ( 6338) hydrogen bonds : bond 0.03051 ( 324) hydrogen bonds : angle 3.45182 ( 924) Misc. bond : bond 0.01196 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 80 time to evaluate : 0.112 Fit side-chains REVERT: B 3 LEU cc_start: 0.7016 (OUTLIER) cc_final: 0.6731 (mp) REVERT: B 55 MET cc_start: 0.8357 (mmm) cc_final: 0.8057 (mmm) REVERT: B 61 LYS cc_start: 0.8204 (tttt) cc_final: 0.7845 (mttp) REVERT: B 90 GLU cc_start: 0.7208 (mm-30) cc_final: 0.6788 (mt-10) REVERT: B 101 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7296 (tm-30) REVERT: D 3 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6715 (mp) REVERT: D 55 MET cc_start: 0.8354 (mmm) cc_final: 0.8054 (mmm) REVERT: D 61 LYS cc_start: 0.8192 (tttt) cc_final: 0.7830 (mttp) REVERT: D 101 GLU cc_start: 0.7829 (OUTLIER) cc_final: 0.7305 (tm-30) outliers start: 17 outliers final: 8 residues processed: 88 average time/residue: 0.4714 time to fit residues: 42.9803 Evaluate side-chains 92 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 6 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3827 r_free = 0.3827 target = 0.163114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.144517 restraints weight = 4307.072| |-----------------------------------------------------------------------------| r_work (start): 0.3609 rms_B_bonded: 1.15 r_work: 0.3502 rms_B_bonded: 1.81 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 3.10 restraints_weight: 0.2500 r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4626 Z= 0.137 Angle : 0.621 6.855 6338 Z= 0.286 Chirality : 0.040 0.128 690 Planarity : 0.006 0.044 792 Dihedral : 10.532 80.593 624 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.36 % Allowed : 1.08 % Favored : 98.57 % Rotamer: Outliers : 2.64 % Allowed : 21.59 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.77 (0.36), residues: 558 helix: 2.88 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.21 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 141 TYR 0.006 0.002 TYR D 130 PHE 0.008 0.001 PHE D 118 TRP 0.008 0.001 TRP A 14 HIS 0.006 0.001 HIS A 58 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 4622) covalent geometry : angle 0.62079 ( 6338) hydrogen bonds : bond 0.03762 ( 324) hydrogen bonds : angle 3.56116 ( 924) Misc. bond : bond 0.01133 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1116 Ramachandran restraints generated. 558 Oldfield, 0 Emsley, 558 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.156 Fit side-chains REVERT: B 3 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6708 (mp) REVERT: B 55 MET cc_start: 0.8411 (mmm) cc_final: 0.8093 (mmm) REVERT: B 61 LYS cc_start: 0.8290 (tttt) cc_final: 0.7858 (mttp) REVERT: B 101 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7337 (tm-30) REVERT: D 3 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6711 (mp) REVERT: D 55 MET cc_start: 0.8413 (mmm) cc_final: 0.8089 (mmm) REVERT: D 61 LYS cc_start: 0.8263 (tttt) cc_final: 0.7842 (mttp) REVERT: D 101 GLU cc_start: 0.7885 (OUTLIER) cc_final: 0.7332 (tm-30) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 0.5310 time to fit residues: 48.3323 Evaluate side-chains 96 residues out of total 454 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 SER Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain B residue 3 LEU Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 101 GLU Chi-restraints excluded: chain C residue 81 SER Chi-restraints excluded: chain C residue 134 THR Chi-restraints excluded: chain D residue 3 LEU Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain D residue 50 THR Chi-restraints excluded: chain D residue 101 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 0.0470 chunk 40 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 3.9990 chunk 1 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3841 r_free = 0.3841 target = 0.164493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.145756 restraints weight = 4358.767| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 1.17 r_work: 0.3514 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3416 rms_B_bonded: 3.14 restraints_weight: 0.2500 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4626 Z= 0.120 Angle : 0.597 6.695 6338 Z= 0.274 Chirality : 0.039 0.125 690 Planarity : 0.006 0.044 792 Dihedral : 10.401 81.591 624 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.36 % Allowed : 0.72 % Favored : 98.92 % Rotamer: Outliers : 2.64 % Allowed : 21.59 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.84 (0.36), residues: 558 helix: 2.93 (0.25), residues: 430 sheet: None (None), residues: 0 loop : 1.23 (0.60), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 141 TYR 0.007 0.001 TYR B 130 PHE 0.007 0.001 PHE A 43 TRP 0.007 0.001 TRP A 14 HIS 0.005 0.001 HIS C 58 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4622) covalent geometry : angle 0.59705 ( 6338) hydrogen bonds : bond 0.03332 ( 324) hydrogen bonds : angle 3.53457 ( 924) Misc. bond : bond 0.00945 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1615.67 seconds wall clock time: 28 minutes 13.49 seconds (1693.49 seconds total)