Starting phenix.real_space_refine on Wed Sep 17 02:56:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tgn_10499/09_2025/6tgn_10499.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tgn_10499/09_2025/6tgn_10499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tgn_10499/09_2025/6tgn_10499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tgn_10499/09_2025/6tgn_10499.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tgn_10499/09_2025/6tgn_10499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tgn_10499/09_2025/6tgn_10499.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 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 1 5.16 5 C 425 2.51 5 N 115 2.21 5 O 131 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 672 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 672 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Time building chain proxies: 0.20, per 1000 atoms: 0.30 Number of scatterers: 672 At special positions: 0 Unit cell: (38.808, 48.51, 51.282, 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 1 16.00 O 131 8.00 N 115 7.00 C 425 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: 0.03 Conformation dependent library (CDL) restraints added in 20.3 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 164 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 2 sheets defined 22.7% alpha, 28.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.03 Creating SS restraints... Processing helix chain 'A' and resid 34 through 46 removed outlier: 3.859A pdb=" N GLU A 40 " --> pdb=" O ALA A 36 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LYS A 41 " --> pdb=" O GLY A 37 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ALA A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 45 " --> pdb=" O LYS A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.864A pdb=" N ASN A 79 " --> pdb=" O PHE A 75 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ARG A 81 " --> pdb=" O VAL A 77 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.553A pdb=" N VAL A 17 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 14 " --> pdb=" O VAL A 17 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.553A pdb=" N VAL A 17 " --> pdb=" O TYR A 14 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 14 " --> pdb=" O VAL A 17 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER A 13 " --> pdb=" O ILE A 87 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N VAL A 89 " --> pdb=" O SER A 13 " (cutoff:3.500A) 17 hydrogen bonds defined for protein. 42 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: 0.05 Time building geometry restraints manager: 0.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 124 1.32 - 1.44: 153 1.44 - 1.56: 399 1.56 - 1.68: 0 1.68 - 1.80: 2 Bond restraints: 678 Sorted by residual: bond pdb=" C TYR A 58 " pdb=" O TYR A 58 " ideal model delta sigma weight residual 1.234 1.197 0.037 1.16e-02 7.43e+03 1.01e+01 bond pdb=" CA ILE A 87 " pdb=" CB ILE A 87 " ideal model delta sigma weight residual 1.537 1.505 0.032 1.26e-02 6.30e+03 6.49e+00 bond pdb=" N ALA A 5 " pdb=" CA ALA A 5 " ideal model delta sigma weight residual 1.458 1.502 -0.044 1.90e-02 2.77e+03 5.31e+00 bond pdb=" C LEU A 56 " pdb=" O LEU A 56 " ideal model delta sigma weight residual 1.236 1.209 0.026 1.21e-02 6.83e+03 4.72e+00 bond pdb=" C ILE A 87 " pdb=" O ILE A 87 " ideal model delta sigma weight residual 1.238 1.214 0.024 1.10e-02 8.26e+03 4.64e+00 ... (remaining 673 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 622 1.53 - 3.07: 215 3.07 - 4.60: 66 4.60 - 6.13: 10 6.13 - 7.66: 3 Bond angle restraints: 916 Sorted by residual: angle pdb=" C ASN A 88 " pdb=" CA ASN A 88 " pdb=" CB ASN A 88 " ideal model delta sigma weight residual 109.53 102.18 7.35 1.65e+00 3.67e-01 1.98e+01 angle pdb=" O GLY A 15 " pdb=" C GLY A 15 " pdb=" N GLY A 16 " ideal model delta sigma weight residual 122.57 126.54 -3.97 9.10e-01 1.21e+00 1.90e+01 angle pdb=" N ILE A 87 " pdb=" CA ILE A 87 " pdb=" C ILE A 87 " ideal model delta sigma weight residual 107.75 113.41 -5.66 1.46e+00 4.69e-01 1.50e+01 angle pdb=" CA LYS A 11 " pdb=" C LYS A 11 " pdb=" O LYS A 11 " ideal model delta sigma weight residual 120.32 116.14 4.18 1.10e+00 8.26e-01 1.44e+01 angle pdb=" N LEU A 85 " pdb=" CA LEU A 85 " pdb=" CB LEU A 85 " ideal model delta sigma weight residual 110.29 105.20 5.09 1.52e+00 4.33e-01 1.12e+01 ... (remaining 911 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 10.12: 333 10.12 - 20.23: 57 20.23 - 30.34: 15 30.34 - 40.45: 4 40.45 - 50.55: 3 Dihedral angle restraints: 412 sinusoidal: 159 harmonic: 253 Sorted by residual: dihedral pdb=" CA ASP A 62 " pdb=" C ASP A 62 " pdb=" N GLY A 63 " pdb=" CA GLY A 63 " ideal model delta harmonic sigma weight residual 180.00 152.99 27.01 0 5.00e+00 4.00e-02 2.92e+01 dihedral pdb=" CA ALA A 5 " pdb=" C ALA A 5 " pdb=" N ASN A 6 " pdb=" CA ASN A 6 " ideal model delta harmonic sigma weight residual -180.00 -159.94 -20.06 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" C ASN A 88 " pdb=" N ASN A 88 " pdb=" CA ASN A 88 " pdb=" CB ASN A 88 " ideal model delta harmonic sigma weight residual -122.60 -112.69 -9.91 0 2.50e+00 1.60e-01 1.57e+01 ... (remaining 409 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.058: 41 0.058 - 0.115: 36 0.115 - 0.172: 17 0.172 - 0.229: 10 0.229 - 0.286: 6 Chirality restraints: 110 Sorted by residual: chirality pdb=" CA VAL A 66 " pdb=" N VAL A 66 " pdb=" C VAL A 66 " pdb=" CB VAL A 66 " both_signs ideal model delta sigma weight residual False 2.44 2.73 -0.29 2.00e-01 2.50e+01 2.05e+00 chirality pdb=" CA ARG A 81 " pdb=" N ARG A 81 " pdb=" C ARG A 81 " pdb=" CB ARG A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CA TYR A 58 " pdb=" N TYR A 58 " pdb=" C TYR A 58 " pdb=" CB TYR A 58 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.85e+00 ... (remaining 107 not shown) Planarity restraints: 120 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 14 " 0.042 2.00e-02 2.50e+03 2.17e-02 9.38e+00 pdb=" CG TYR A 14 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TYR A 14 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 14 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR A 14 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 14 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 14 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 14 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 58 " -0.030 2.00e-02 2.50e+03 1.63e-02 5.33e+00 pdb=" CG TYR A 58 " 0.012 2.00e-02 2.50e+03 pdb=" CD1 TYR A 58 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 58 " 0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR A 58 " 0.012 2.00e-02 2.50e+03 pdb=" CE2 TYR A 58 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 58 " -0.015 2.00e-02 2.50e+03 pdb=" OH TYR A 58 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 46 " 0.001 2.00e-02 2.50e+03 1.71e-02 5.12e+00 pdb=" CG PHE A 46 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 PHE A 46 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 PHE A 46 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE A 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 46 " 0.014 2.00e-02 2.50e+03 pdb=" CZ PHE A 46 " -0.019 2.00e-02 2.50e+03 ... (remaining 117 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 41 2.71 - 3.26: 598 3.26 - 3.80: 901 3.80 - 4.35: 1146 4.35 - 4.90: 1881 Nonbonded interactions: 4567 Sorted by model distance: nonbonded pdb=" OD1 ASP A 60 " pdb=" N GLU A 61 " model vdw 2.161 3.120 nonbonded pdb=" N ASP A 60 " pdb=" O ASP A 60 " model vdw 2.548 2.496 nonbonded pdb=" N ARG A 19 " pdb=" O ARG A 19 " model vdw 2.602 2.496 nonbonded pdb=" N GLU A 34 " pdb=" OE1 GLU A 34 " model vdw 2.607 3.120 nonbonded pdb=" O ARG A 19 " pdb=" CA ARG A 20 " model vdw 2.627 2.776 ... (remaining 4562 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.070 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: 0.010 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 1.920 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 3.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 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 : 0.010 0.044 678 Z= 0.609 Angle : 1.727 7.656 916 Z= 1.087 Chirality : 0.118 0.286 110 Planarity : 0.008 0.022 120 Dihedral : 11.933 50.555 248 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.39 % Allowed : 2.78 % Favored : 95.83 % 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: -3.57 (0.75), residues: 86 helix: -4.95 (0.26), residues: 18 sheet: -1.43 (0.99), residues: 28 loop : -1.61 (0.75), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.006 ARG A 19 TYR 0.042 0.016 TYR A 14 PHE 0.030 0.008 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00962 ( 678) covalent geometry : angle 1.72677 ( 916) hydrogen bonds : bond 0.27118 ( 17) hydrogen bonds : angle 11.05327 ( 42) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.014 Fit side-chains revert: symmetry clash REVERT: A 17 VAL cc_start: 0.9635 (t) cc_final: 0.9428 (p) REVERT: A 22 ARG cc_start: 0.9505 (mtp-110) cc_final: 0.9078 (mpt180) REVERT: A 34 GLU cc_start: 0.9286 (pm20) cc_final: 0.8982 (mp0) REVERT: A 35 MET cc_start: 0.8809 (mmm) cc_final: 0.7750 (mmm) REVERT: A 59 SER cc_start: 0.9144 (m) cc_final: 0.8752 (t) REVERT: A 62 ASP cc_start: 0.8422 (p0) cc_final: 0.8135 (p0) REVERT: A 70 ASP cc_start: 0.8954 (p0) cc_final: 0.8753 (p0) outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.0411 time to fit residues: 1.6105 Evaluate side-chains 34 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 9.9990 overall best weight: 5.2490 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.104377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.088623 restraints weight = 1497.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.091197 restraints weight = 892.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.092821 restraints weight = 627.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.094016 restraints weight = 492.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.094908 restraints weight = 409.100| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 678 Z= 0.140 Angle : 0.637 5.431 916 Z= 0.322 Chirality : 0.044 0.129 110 Planarity : 0.003 0.014 120 Dihedral : 7.322 41.701 97 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.56 % Allowed : 15.28 % Favored : 79.17 % 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: -2.57 (0.77), residues: 86 helix: -3.09 (0.81), residues: 20 sheet: -1.11 (1.00), residues: 28 loop : -1.15 (0.76), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 22 TYR 0.011 0.002 TYR A 58 PHE 0.009 0.002 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 678) covalent geometry : angle 0.63695 ( 916) hydrogen bonds : bond 0.03572 ( 17) hydrogen bonds : angle 6.54043 ( 42) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8043 (mmm) cc_final: 0.7163 (mmm) REVERT: A 88 ASN cc_start: 0.8433 (m-40) cc_final: 0.8198 (t0) outliers start: 4 outliers final: 2 residues processed: 34 average time/residue: 0.0396 time to fit residues: 1.4269 Evaluate side-chains 31 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 29 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 overall best weight: 8.2492 ------------------------------------------------------------------------------- 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 = 0.3389 r_free = 0.3389 target = 0.104914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.090263 restraints weight = 1478.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.092626 restraints weight = 801.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094341 restraints weight = 566.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.095252 restraints weight = 442.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.096134 restraints weight = 380.366| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 678 Z= 0.199 Angle : 0.731 8.251 916 Z= 0.352 Chirality : 0.043 0.130 110 Planarity : 0.003 0.009 120 Dihedral : 7.407 43.109 97 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 6.94 % Allowed : 18.06 % Favored : 75.00 % 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: -0.95 (0.94), residues: 86 helix: -2.09 (1.27), residues: 14 sheet: -0.72 (1.03), residues: 28 loop : 0.15 (1.01), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 19 TYR 0.011 0.002 TYR A 58 PHE 0.019 0.003 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 678) covalent geometry : angle 0.73092 ( 916) hydrogen bonds : bond 0.03408 ( 17) hydrogen bonds : angle 6.54793 ( 42) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 29 time to evaluate : 0.015 Fit side-chains REVERT: A 35 MET cc_start: 0.8192 (mmm) cc_final: 0.7630 (mmm) REVERT: A 71 ASP cc_start: 0.8278 (t0) cc_final: 0.7930 (t0) outliers start: 5 outliers final: 2 residues processed: 33 average time/residue: 0.0454 time to fit residues: 1.5823 Evaluate side-chains 26 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 4 optimal weight: 8.9990 chunk 5 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 overall best weight: 5.6988 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.106889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.092064 restraints weight = 1521.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.094266 restraints weight = 860.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.095856 restraints weight = 621.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 20)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.096577 restraints weight = 493.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.097523 restraints weight = 438.022| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.5446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 678 Z= 0.147 Angle : 0.722 8.889 916 Z= 0.341 Chirality : 0.043 0.121 110 Planarity : 0.002 0.010 120 Dihedral : 7.038 43.102 97 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 6.94 % Allowed : 23.61 % Favored : 69.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.99), residues: 86 helix: -2.02 (1.40), residues: 14 sheet: -0.58 (0.93), residues: 34 loop : 1.28 (1.16), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 22 TYR 0.011 0.002 TYR A 58 PHE 0.012 0.002 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 678) covalent geometry : angle 0.72211 ( 916) hydrogen bonds : bond 0.02915 ( 17) hydrogen bonds : angle 5.82694 ( 42) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.027 Fit side-chains REVERT: A 21 PHE cc_start: 0.8969 (p90) cc_final: 0.8291 (p90) REVERT: A 35 MET cc_start: 0.8065 (mmm) cc_final: 0.7748 (mmm) REVERT: A 39 LYS cc_start: 0.8867 (mtmm) cc_final: 0.8423 (mtmm) outliers start: 5 outliers final: 4 residues processed: 34 average time/residue: 0.0457 time to fit residues: 1.6476 Evaluate side-chains 34 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 30 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 5.9990 overall best weight: 6.4990 ------------------------------------------------------------------------------- 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 = 0.3422 r_free = 0.3422 target = 0.107204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.092518 restraints weight = 1510.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.095058 restraints weight = 825.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.096741 restraints weight = 557.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098041 restraints weight = 426.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.099004 restraints weight = 349.461| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 678 Z= 0.156 Angle : 0.725 8.932 916 Z= 0.331 Chirality : 0.043 0.118 110 Planarity : 0.002 0.006 120 Dihedral : 7.202 43.755 97 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 9.72 % Allowed : 25.00 % Favored : 65.28 % 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: -0.25 (0.99), residues: 86 helix: -2.51 (1.28), residues: 14 sheet: -0.35 (0.95), residues: 34 loop : 1.33 (1.14), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 22 TYR 0.010 0.002 TYR A 58 PHE 0.013 0.002 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00342 ( 678) covalent geometry : angle 0.72531 ( 916) hydrogen bonds : bond 0.02869 ( 17) hydrogen bonds : angle 5.96492 ( 42) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.015 Fit side-chains REVERT: A 35 MET cc_start: 0.8140 (mmm) cc_final: 0.7725 (mmm) REVERT: A 39 LYS cc_start: 0.8967 (mtmm) cc_final: 0.8625 (mtmm) outliers start: 7 outliers final: 6 residues processed: 33 average time/residue: 0.0434 time to fit residues: 1.5142 Evaluate side-chains 35 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 29 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 0.0570 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 overall best weight: 12.5140 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.103622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.088715 restraints weight = 1575.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.091008 restraints weight = 929.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.092708 restraints weight = 658.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093847 restraints weight = 511.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.094629 restraints weight = 427.286| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.6006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 678 Z= 0.284 Angle : 0.852 8.894 916 Z= 0.400 Chirality : 0.046 0.151 110 Planarity : 0.004 0.017 120 Dihedral : 7.691 44.236 97 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 9.72 % Allowed : 25.00 % Favored : 65.28 % 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: -0.80 (0.98), residues: 86 helix: -2.98 (1.20), residues: 14 sheet: -0.78 (0.95), residues: 34 loop : 1.10 (1.13), residues: 38 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 22 TYR 0.010 0.002 TYR A 58 PHE 0.020 0.003 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00620 ( 678) covalent geometry : angle 0.85172 ( 916) hydrogen bonds : bond 0.03789 ( 17) hydrogen bonds : angle 6.71754 ( 42) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.015 Fit side-chains REVERT: A 35 MET cc_start: 0.8403 (mmm) cc_final: 0.7706 (mmm) outliers start: 7 outliers final: 6 residues processed: 33 average time/residue: 0.0396 time to fit residues: 1.3880 Evaluate side-chains 33 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 8.9990 chunk 3 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 = 0.3417 r_free = 0.3417 target = 0.106028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.090641 restraints weight = 1534.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.092895 restraints weight = 922.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094451 restraints weight = 663.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.095622 restraints weight = 530.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.096454 restraints weight = 448.270| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.6171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 678 Z= 0.156 Angle : 0.808 8.550 916 Z= 0.362 Chirality : 0.045 0.155 110 Planarity : 0.002 0.011 120 Dihedral : 7.031 43.369 97 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 8.33 % Allowed : 27.78 % Favored : 63.89 % 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: -0.90 (0.98), residues: 86 helix: -2.75 (1.07), residues: 20 sheet: -0.53 (0.96), residues: 34 loop : 1.30 (1.23), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 20 TYR 0.012 0.002 TYR A 58 PHE 0.011 0.002 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 678) covalent geometry : angle 0.80809 ( 916) hydrogen bonds : bond 0.02859 ( 17) hydrogen bonds : angle 5.86748 ( 42) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.014 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 34 average time/residue: 0.0424 time to fit residues: 1.5246 Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 20 ARG Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 30.0000 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 8.9990 chunk 7 optimal weight: 4.9990 overall best weight: 5.2490 ------------------------------------------------------------------------------- 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 = 0.3427 r_free = 0.3427 target = 0.105786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.090939 restraints weight = 1492.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.093249 restraints weight = 837.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.094822 restraints weight = 588.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.095824 restraints weight = 464.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.096697 restraints weight = 399.665| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 678 Z= 0.143 Angle : 0.824 9.358 916 Z= 0.366 Chirality : 0.044 0.147 110 Planarity : 0.003 0.019 120 Dihedral : 6.811 43.316 97 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 8.33 % Allowed : 30.56 % Favored : 61.11 % 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: -0.60 (0.99), residues: 86 helix: -2.63 (1.06), residues: 20 sheet: -0.21 (0.98), residues: 34 loop : 1.38 (1.24), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 20 TYR 0.011 0.002 TYR A 58 PHE 0.010 0.002 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 678) covalent geometry : angle 0.82392 ( 916) hydrogen bonds : bond 0.02726 ( 17) hydrogen bonds : angle 5.86643 ( 42) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.014 Fit side-chains REVERT: A 35 MET cc_start: 0.8027 (mmm) cc_final: 0.7377 (mmm) REVERT: A 39 LYS cc_start: 0.8949 (mtmm) cc_final: 0.8237 (mtmm) outliers start: 6 outliers final: 4 residues processed: 33 average time/residue: 0.0405 time to fit residues: 1.4183 Evaluate side-chains 35 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 4 optimal weight: 9.9990 chunk 5 optimal weight: 20.0000 chunk 6 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 overall best weight: 8.7490 ------------------------------------------------------------------------------- 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 = 0.3414 r_free = 0.3414 target = 0.105407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.090203 restraints weight = 1530.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.092589 restraints weight = 929.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.094224 restraints weight = 661.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.095330 restraints weight = 525.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.096148 restraints weight = 444.990| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.6451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 678 Z= 0.216 Angle : 0.891 9.067 916 Z= 0.414 Chirality : 0.046 0.151 110 Planarity : 0.003 0.017 120 Dihedral : 4.968 15.236 93 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 8.33 % Allowed : 29.17 % Favored : 62.50 % 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: -0.59 (1.02), residues: 86 helix: -2.51 (1.13), residues: 20 sheet: -0.32 (1.00), residues: 34 loop : 1.46 (1.27), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 22 TYR 0.011 0.002 TYR A 58 PHE 0.015 0.002 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00498 ( 678) covalent geometry : angle 0.89073 ( 916) hydrogen bonds : bond 0.03408 ( 17) hydrogen bonds : angle 6.78909 ( 42) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 32 time to evaluate : 0.015 Fit side-chains REVERT: A 35 MET cc_start: 0.8141 (mmm) cc_final: 0.7525 (mmm) outliers start: 6 outliers final: 4 residues processed: 34 average time/residue: 0.0411 time to fit residues: 1.4829 Evaluate side-chains 36 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 6.9990 chunk 3 optimal weight: 20.0000 chunk 4 optimal weight: 0.0870 chunk 5 optimal weight: 8.9990 chunk 6 optimal weight: 20.0000 chunk 7 optimal weight: 3.9990 overall best weight: 4.2710 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.108682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.093959 restraints weight = 1453.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.096383 restraints weight = 851.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.098120 restraints weight = 595.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.099132 restraints weight = 461.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.100105 restraints weight = 389.549| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.6773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 678 Z= 0.175 Angle : 0.975 9.260 916 Z= 0.441 Chirality : 0.046 0.156 110 Planarity : 0.002 0.008 120 Dihedral : 4.810 21.654 93 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 5.56 % Allowed : 34.72 % Favored : 59.72 % 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: -0.35 (1.02), residues: 86 helix: -2.52 (1.12), residues: 20 sheet: -0.07 (0.99), residues: 34 loop : 1.62 (1.29), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 22 TYR 0.011 0.002 TYR A 58 PHE 0.008 0.002 PHE A 46 Details of bonding type rmsd covalent geometry : bond 0.00466 ( 678) covalent geometry : angle 0.97523 ( 916) hydrogen bonds : bond 0.03237 ( 17) hydrogen bonds : angle 6.35945 ( 42) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 172 Ramachandran restraints generated. 86 Oldfield, 0 Emsley, 86 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.051 Fit side-chains REVERT: A 35 MET cc_start: 0.7862 (mmm) cc_final: 0.7397 (mmm) outliers start: 4 outliers final: 3 residues processed: 36 average time/residue: 0.0831 time to fit residues: 3.1791 Evaluate side-chains 35 residues out of total 72 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 32 time to evaluate : 0.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 VAL Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 85 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 8 random chunks: chunk 0 optimal weight: 20.0000 chunk 1 optimal weight: 8.9990 chunk 2 optimal weight: 5.9990 chunk 3 optimal weight: 0.3980 chunk 4 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 = 0.3453 r_free = 0.3453 target = 0.107919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.091898 restraints weight = 1507.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.094155 restraints weight = 913.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095777 restraints weight = 662.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.096998 restraints weight = 530.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.097838 restraints weight = 451.045| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 678 Z= 0.167 Angle : 0.975 9.725 916 Z= 0.440 Chirality : 0.045 0.147 110 Planarity : 0.002 0.010 120 Dihedral : 4.491 19.529 93 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 6.94 % Allowed : 31.94 % Favored : 61.11 % 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: -0.26 (1.01), residues: 86 helix: -2.49 (1.14), residues: 20 sheet: 0.00 (0.96), residues: 34 loop : 1.67 (1.28), residues: 32 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 22 TYR 0.011 0.002 TYR A 58 PHE 0.009 0.002 PHE A 21 Details of bonding type rmsd covalent geometry : bond 0.00444 ( 678) covalent geometry : angle 0.97504 ( 916) hydrogen bonds : bond 0.03961 ( 17) hydrogen bonds : angle 6.66082 ( 42) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 223.46 seconds wall clock time: 4 minutes 43.99 seconds (283.99 seconds total)