Starting phenix.real_space_refine on Wed Jun 4 11:18:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7t2e_25611/06_2025/7t2e_25611.cif Found real_map, /net/cci-nas-00/data/ceres_data/7t2e_25611/06_2025/7t2e_25611.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7t2e_25611/06_2025/7t2e_25611.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7t2e_25611/06_2025/7t2e_25611.map" model { file = "/net/cci-nas-00/data/ceres_data/7t2e_25611/06_2025/7t2e_25611.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7t2e_25611/06_2025/7t2e_25611.cif" } resolution = 2.7 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1500 2.51 5 N 404 2.21 5 O 480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 2390 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1195 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Chain: "B" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1195 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 9, 'TRANS': 146} Time building chain proxies: 2.15, per 1000 atoms: 0.90 Number of scatterers: 2390 At special positions: 0 Unit cell: (61.6, 77, 108.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 480 8.00 N 404 7.00 C 1500 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: 0.54 Conformation dependent library (CDL) restraints added in 286.7 milliseconds 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 564 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 4 sheets defined 12.8% alpha, 36.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 90 through 103 Processing helix chain 'A' and resid 151 through 156 Processing helix chain 'B' and resid 90 through 103 Processing helix chain 'B' and resid 151 through 156 Processing sheet with id=AA1, first strand: chain 'A' and resid 36 through 38 removed outlier: 5.634A pdb=" N ALA A 107 " --> pdb=" O TYR A 20 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N LYS A 142 " --> pdb=" O SER A 125 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 127 " --> pdb=" O THR A 140 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N THR A 140 " --> pdb=" O ILE A 127 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS A 129 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N THR A 138 " --> pdb=" O LYS A 129 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N VAL A 131 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N VAL A 136 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N SER A 81 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N LEU A 45 " --> pdb=" O SER A 81 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N THR A 83 " --> pdb=" O LYS A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 51 through 56 removed outlier: 6.681A pdb=" N THR A 51 " --> pdb=" O LYS A 75 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS A 75 " --> pdb=" O THR A 51 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N GLU A 53 " --> pdb=" O GLY A 73 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 36 through 38 removed outlier: 5.506A pdb=" N ALA B 107 " --> pdb=" O TYR B 20 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N LYS B 142 " --> pdb=" O SER B 125 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N ILE B 127 " --> pdb=" O THR B 140 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N THR B 140 " --> pdb=" O ILE B 127 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N LYS B 129 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N THR B 138 " --> pdb=" O LYS B 129 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N VAL B 131 " --> pdb=" O VAL B 136 " (cutoff:3.500A) removed outlier: 8.643A pdb=" N VAL B 136 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N SER B 81 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU B 45 " --> pdb=" O SER B 81 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N THR B 83 " --> pdb=" O LYS B 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.665A pdb=" N THR B 51 " --> pdb=" O LYS B 75 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LYS B 75 " --> pdb=" O THR B 51 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU B 53 " --> pdb=" O GLY B 73 " (cutoff:3.500A) 78 hydrogen bonds defined for protein. 204 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: 0.51 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 788 1.34 - 1.46: 564 1.46 - 1.58: 1086 1.58 - 1.69: 0 1.69 - 1.81: 12 Bond restraints: 2450 Sorted by residual: bond pdb=" CA GLY A 22 " pdb=" C GLY A 22 " ideal model delta sigma weight residual 1.519 1.512 0.007 8.90e-03 1.26e+04 5.52e-01 bond pdb=" CA ASP A 25 " pdb=" CB ASP A 25 " ideal model delta sigma weight residual 1.528 1.518 0.009 1.50e-02 4.44e+03 3.86e-01 bond pdb=" CG PRO A 113 " pdb=" CD PRO A 113 " ideal model delta sigma weight residual 1.503 1.486 0.017 3.40e-02 8.65e+02 2.65e-01 bond pdb=" CB LYS A 109 " pdb=" CG LYS A 109 " ideal model delta sigma weight residual 1.520 1.505 0.015 3.00e-02 1.11e+03 2.50e-01 bond pdb=" CA LYS A 21 " pdb=" C LYS A 21 " ideal model delta sigma weight residual 1.523 1.530 -0.008 1.61e-02 3.86e+03 2.33e-01 ... (remaining 2445 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.84: 3066 0.84 - 1.68: 219 1.68 - 2.52: 27 2.52 - 3.36: 23 3.36 - 4.20: 7 Bond angle restraints: 3342 Sorted by residual: angle pdb=" C VAL B 34 " pdb=" N ASP B 35 " pdb=" CA ASP B 35 " ideal model delta sigma weight residual 122.74 125.43 -2.69 1.44e+00 4.82e-01 3.50e+00 angle pdb=" C GLY A 147 " pdb=" N ARG A 148 " pdb=" CA ARG A 148 " ideal model delta sigma weight residual 121.61 124.16 -2.55 1.39e+00 5.18e-01 3.36e+00 angle pdb=" N PHE A 82 " pdb=" CA PHE A 82 " pdb=" C PHE A 82 " ideal model delta sigma weight residual 109.14 111.70 -2.56 1.49e+00 4.50e-01 2.95e+00 angle pdb=" CA TRP B 99 " pdb=" CB TRP B 99 " pdb=" CG TRP B 99 " ideal model delta sigma weight residual 113.60 116.59 -2.99 1.90e+00 2.77e-01 2.48e+00 angle pdb=" N GLY B 122 " pdb=" CA GLY B 122 " pdb=" C GLY B 122 " ideal model delta sigma weight residual 110.55 113.11 -2.56 1.64e+00 3.72e-01 2.43e+00 ... (remaining 3337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.87: 1252 16.87 - 33.73: 130 33.73 - 50.59: 48 50.59 - 67.46: 9 67.46 - 84.32: 1 Dihedral angle restraints: 1440 sinusoidal: 556 harmonic: 884 Sorted by residual: dihedral pdb=" CA ASP A 79 " pdb=" CB ASP A 79 " pdb=" CG ASP A 79 " pdb=" OD1 ASP A 79 " ideal model delta sinusoidal sigma weight residual -30.00 -89.60 59.60 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" CA LYS A 109 " pdb=" C LYS A 109 " pdb=" N ILE A 110 " pdb=" CA ILE A 110 " ideal model delta harmonic sigma weight residual 180.00 164.47 15.53 0 5.00e+00 4.00e-02 9.64e+00 dihedral pdb=" CB GLU B 135 " pdb=" CG GLU B 135 " pdb=" CD GLU B 135 " pdb=" OE1 GLU B 135 " ideal model delta sinusoidal sigma weight residual 0.00 -84.32 84.32 1 3.00e+01 1.11e-03 9.61e+00 ... (remaining 1437 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 209 0.028 - 0.057: 95 0.057 - 0.085: 23 0.085 - 0.113: 29 0.113 - 0.141: 8 Chirality restraints: 364 Sorted by residual: chirality pdb=" CA ILE A 127 " pdb=" N ILE A 127 " pdb=" C ILE A 127 " pdb=" CB ILE A 127 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE B 127 " pdb=" N ILE B 127 " pdb=" C ILE B 127 " pdb=" CB ILE B 127 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA VAL B 3 " pdb=" N VAL B 3 " pdb=" C VAL B 3 " pdb=" CB VAL B 3 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 361 not shown) Planarity restraints: 434 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 112 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO A 113 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 113 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 113 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 8 " 0.017 5.00e-02 4.00e+02 2.58e-02 1.07e+00 pdb=" N PRO A 9 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO A 9 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 9 " 0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET B 8 " 0.014 5.00e-02 4.00e+02 2.10e-02 7.04e-01 pdb=" N PRO B 9 " -0.036 5.00e-02 4.00e+02 pdb=" CA PRO B 9 " 0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 9 " 0.012 5.00e-02 4.00e+02 ... (remaining 431 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 419 2.77 - 3.30: 1887 3.30 - 3.84: 3607 3.84 - 4.37: 3992 4.37 - 4.90: 7404 Nonbonded interactions: 17309 Sorted by model distance: nonbonded pdb=" OH TYR B 108 " pdb=" OD1 ASN B 145 " model vdw 2.242 3.040 nonbonded pdb=" OH TYR A 108 " pdb=" OD1 ASN A 145 " model vdw 2.307 3.040 nonbonded pdb=" O THR A 157 " pdb=" OG1 THR A 157 " model vdw 2.489 3.040 nonbonded pdb=" O SER A 156 " pdb=" OG1 THR A 157 " model vdw 2.498 3.040 nonbonded pdb=" O PRO B 30 " pdb=" NZ LYS B 109 " model vdw 2.538 3.120 ... (remaining 17304 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 'B' } 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: 0.790 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 10.770 Find NCS groups from input model: 0.070 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:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2450 Z= 0.128 Angle : 0.540 4.198 3342 Z= 0.297 Chirality : 0.045 0.141 364 Planarity : 0.004 0.032 434 Dihedral : 16.112 84.321 876 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer: Outliers : 1.18 % Allowed : 22.83 % Favored : 75.98 % 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: 0.14 (0.45), residues: 308 helix: 1.97 (1.05), residues: 28 sheet: -0.11 (0.39), residues: 158 loop : 0.17 (0.50), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 18 PHE 0.012 0.002 PHE B 120 TYR 0.009 0.001 TYR A 108 ARG 0.001 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.14774 ( 78) hydrogen bonds : angle 5.69209 ( 204) covalent geometry : bond 0.00280 ( 2450) covalent geometry : angle 0.53950 ( 3342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.289 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 37 average time/residue: 1.4604 time to fit residues: 55.1698 Evaluate side-chains 38 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 36 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 12 optimal weight: 0.5980 chunk 7 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.109589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.088110 restraints weight = 2935.231| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.12 r_work: 0.2886 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.0666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2450 Z= 0.203 Angle : 0.585 4.936 3342 Z= 0.308 Chirality : 0.048 0.156 364 Planarity : 0.004 0.036 434 Dihedral : 5.817 48.169 339 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 3.54 % Allowed : 20.87 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.47), residues: 308 helix: 2.06 (1.10), residues: 28 sheet: -0.14 (0.40), residues: 158 loop : 0.31 (0.52), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 18 PHE 0.017 0.003 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 78) hydrogen bonds : angle 5.34509 ( 204) covalent geometry : bond 0.00510 ( 2450) covalent geometry : angle 0.58485 ( 3342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.262 Fit side-chains REVERT: A 31 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8343 (mm) outliers start: 9 outliers final: 4 residues processed: 39 average time/residue: 1.5049 time to fit residues: 59.8963 Evaluate side-chains 41 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 23 optimal weight: 2.9990 chunk 6 optimal weight: 0.0060 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 0.8980 overall best weight: 1.5802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.111183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.089546 restraints weight = 2925.274| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 2.13 r_work: 0.2861 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2752 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.0681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2450 Z= 0.136 Angle : 0.508 4.233 3342 Z= 0.267 Chirality : 0.046 0.147 364 Planarity : 0.004 0.031 434 Dihedral : 5.004 45.548 336 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 1.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.97 % Allowed : 22.44 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.47), residues: 308 helix: 2.24 (1.07), residues: 28 sheet: -0.10 (0.40), residues: 158 loop : 0.47 (0.53), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 18 PHE 0.013 0.002 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.001 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03562 ( 78) hydrogen bonds : angle 5.10013 ( 204) covalent geometry : bond 0.00335 ( 2450) covalent geometry : angle 0.50838 ( 3342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.291 Fit side-chains REVERT: A 31 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8339 (mm) outliers start: 5 outliers final: 3 residues processed: 51 average time/residue: 1.1838 time to fit residues: 61.8102 Evaluate side-chains 49 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.109689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.088284 restraints weight = 2936.307| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 2.12 r_work: 0.2889 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2450 Z= 0.186 Angle : 0.558 4.451 3342 Z= 0.293 Chirality : 0.048 0.154 364 Planarity : 0.004 0.035 434 Dihedral : 4.555 17.769 334 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.36 % Allowed : 22.05 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.47), residues: 308 helix: 2.02 (1.05), residues: 28 sheet: -0.14 (0.40), residues: 158 loop : 0.37 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 18 PHE 0.016 0.003 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 78) hydrogen bonds : angle 5.20816 ( 204) covalent geometry : bond 0.00468 ( 2450) covalent geometry : angle 0.55806 ( 3342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.292 Fit side-chains REVERT: A 31 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8344 (mm) outliers start: 6 outliers final: 5 residues processed: 42 average time/residue: 1.4140 time to fit residues: 60.6839 Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.110495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.088794 restraints weight = 3016.907| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.16 r_work: 0.2893 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.0835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2450 Z= 0.149 Angle : 0.516 4.455 3342 Z= 0.272 Chirality : 0.046 0.149 364 Planarity : 0.004 0.033 434 Dihedral : 4.373 17.027 334 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 21.65 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.47), residues: 308 helix: 2.12 (1.05), residues: 28 sheet: -0.11 (0.40), residues: 158 loop : 0.42 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 PHE 0.014 0.002 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 78) hydrogen bonds : angle 5.12139 ( 204) covalent geometry : bond 0.00372 ( 2450) covalent geometry : angle 0.51595 ( 3342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.280 Fit side-chains REVERT: A 31 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8340 (mm) outliers start: 7 outliers final: 6 residues processed: 42 average time/residue: 1.4798 time to fit residues: 63.4407 Evaluate side-chains 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 63 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 9 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 12 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.088820 restraints weight = 2955.535| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 2.13 r_work: 0.2896 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2450 Z= 0.150 Angle : 0.517 4.462 3342 Z= 0.272 Chirality : 0.047 0.149 364 Planarity : 0.004 0.033 434 Dihedral : 4.367 17.049 334 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 21.65 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.47), residues: 308 helix: 2.12 (1.04), residues: 28 sheet: -0.13 (0.40), residues: 158 loop : 0.40 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 PHE 0.014 0.002 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 78) hydrogen bonds : angle 5.10990 ( 204) covalent geometry : bond 0.00374 ( 2450) covalent geometry : angle 0.51716 ( 3342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.275 Fit side-chains REVERT: A 31 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8337 (mm) outliers start: 7 outliers final: 5 residues processed: 42 average time/residue: 1.4907 time to fit residues: 63.9008 Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 0.6980 chunk 26 optimal weight: 0.2980 chunk 5 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.110034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.088484 restraints weight = 2995.141| |-----------------------------------------------------------------------------| r_work (start): 0.2950 rms_B_bonded: 2.14 r_work: 0.2836 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2450 Z= 0.163 Angle : 0.528 4.505 3342 Z= 0.277 Chirality : 0.047 0.150 364 Planarity : 0.004 0.035 434 Dihedral : 4.412 17.301 334 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.15 % Allowed : 22.05 % Favored : 74.80 % 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: 0.22 (0.47), residues: 308 helix: 2.09 (1.04), residues: 28 sheet: -0.15 (0.40), residues: 158 loop : 0.33 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 PHE 0.015 0.003 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 78) hydrogen bonds : angle 5.12700 ( 204) covalent geometry : bond 0.00407 ( 2450) covalent geometry : angle 0.52771 ( 3342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.296 Fit side-chains REVERT: A 31 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8370 (mm) outliers start: 8 outliers final: 5 residues processed: 43 average time/residue: 1.4103 time to fit residues: 61.9143 Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 29 optimal weight: 0.0070 chunk 12 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 overall best weight: 1.7602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.110351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.088620 restraints weight = 3048.887| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 2.17 r_work: 0.2836 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2450 Z= 0.148 Angle : 0.517 4.450 3342 Z= 0.271 Chirality : 0.046 0.148 364 Planarity : 0.004 0.035 434 Dihedral : 4.344 16.968 334 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.76 % Allowed : 22.44 % Favored : 74.80 % 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: 0.23 (0.47), residues: 308 helix: 2.09 (1.03), residues: 28 sheet: -0.13 (0.40), residues: 158 loop : 0.33 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 18 PHE 0.014 0.002 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03575 ( 78) hydrogen bonds : angle 5.10668 ( 204) covalent geometry : bond 0.00369 ( 2450) covalent geometry : angle 0.51657 ( 3342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.284 Fit side-chains REVERT: A 31 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8359 (mm) outliers start: 7 outliers final: 5 residues processed: 40 average time/residue: 1.4227 time to fit residues: 58.0914 Evaluate side-chains 45 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 4 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 7 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.109822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.088364 restraints weight = 2979.141| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 2.13 r_work: 0.2887 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.0895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2450 Z= 0.171 Angle : 0.537 4.524 3342 Z= 0.282 Chirality : 0.047 0.151 364 Planarity : 0.004 0.037 434 Dihedral : 4.442 17.487 334 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 3.54 % Allowed : 21.65 % Favored : 74.80 % 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: 0.18 (0.47), residues: 308 helix: 2.06 (1.03), residues: 28 sheet: -0.15 (0.40), residues: 158 loop : 0.27 (0.54), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 18 PHE 0.015 0.003 PHE A 120 TYR 0.007 0.001 TYR A 108 ARG 0.002 0.000 ARG A 155 Details of bonding type rmsd hydrogen bonds : bond 0.03792 ( 78) hydrogen bonds : angle 5.15469 ( 204) covalent geometry : bond 0.00429 ( 2450) covalent geometry : angle 0.53679 ( 3342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 39 time to evaluate : 0.260 Fit side-chains REVERT: A 31 LEU cc_start: 0.8672 (OUTLIER) cc_final: 0.8352 (mm) outliers start: 9 outliers final: 6 residues processed: 43 average time/residue: 1.3414 time to fit residues: 58.9041 Evaluate side-chains 46 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Chi-restraints excluded: chain A residue 109 LYS Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 136 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 0.1980 chunk 10 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 11 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.112451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.090926 restraints weight = 2947.753| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 2.14 r_work: 0.2923 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2816 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.0881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2450 Z= 0.086 Angle : 0.455 4.156 3342 Z= 0.238 Chirality : 0.044 0.143 364 Planarity : 0.003 0.033 434 Dihedral : 3.940 14.631 334 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 2.36 % Allowed : 22.83 % Favored : 74.80 % 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: 0.36 (0.47), residues: 308 helix: 2.37 (1.01), residues: 28 sheet: -0.09 (0.40), residues: 158 loop : 0.43 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 123 PHE 0.009 0.002 PHE B 120 TYR 0.006 0.001 TYR A 108 ARG 0.001 0.000 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.02874 ( 78) hydrogen bonds : angle 4.85475 ( 204) covalent geometry : bond 0.00205 ( 2450) covalent geometry : angle 0.45543 ( 3342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 616 Ramachandran restraints generated. 308 Oldfield, 0 Emsley, 308 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.285 Fit side-chains REVERT: A 31 LEU cc_start: 0.8609 (OUTLIER) cc_final: 0.8316 (mm) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 1.3457 time to fit residues: 59.1804 Evaluate side-chains 44 residues out of total 254 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 44 ASP Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 57 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 6.9990 chunk 3 optimal weight: 5.9990 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 15 optimal weight: 6.9990 chunk 10 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 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 29 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.113634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.092098 restraints weight = 3004.871| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 2.16 r_work: 0.2945 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 2450 Z= 0.082 Angle : 0.436 4.115 3342 Z= 0.227 Chirality : 0.044 0.142 364 Planarity : 0.003 0.030 434 Dihedral : 3.688 11.762 334 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer: Outliers : 1.57 % Allowed : 23.62 % Favored : 74.80 % 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: 0.51 (0.47), residues: 308 helix: 2.58 (1.00), residues: 28 sheet: -0.05 (0.40), residues: 158 loop : 0.59 (0.55), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 123 PHE 0.008 0.002 PHE B 120 TYR 0.006 0.001 TYR A 108 ARG 0.001 0.000 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.02668 ( 78) hydrogen bonds : angle 4.67331 ( 204) covalent geometry : bond 0.00193 ( 2450) covalent geometry : angle 0.43604 ( 3342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2415.61 seconds wall clock time: 41 minutes 54.75 seconds (2514.75 seconds total)