Starting phenix.real_space_refine on Fri Aug 22 12:36:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ihv_35460/08_2025/8ihv_35460.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ihv_35460/08_2025/8ihv_35460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ihv_35460/08_2025/8ihv_35460.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ihv_35460/08_2025/8ihv_35460.map" model { file = "/net/cci-nas-00/data/ceres_data/8ihv_35460/08_2025/8ihv_35460.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ihv_35460/08_2025/8ihv_35460.cif" } resolution = 3.11 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= 0.001 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 864 2.51 5 N 261 2.21 5 O 315 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1446 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 482 Classifications: {'peptide': 69} Link IDs: {'TRANS': 68} Restraints were copied for chains: B, C Time building chain proxies: 0.29, per 1000 atoms: 0.20 Number of scatterers: 1446 At special positions: 0 Unit cell: (78.12, 63, 37.8, 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 315 8.00 N 261 7.00 C 864 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: 0.21 Conformation dependent library (CDL) restraints added in 36.1 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 348 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 5 sheets defined 0.0% alpha, 13.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 97 through 99 Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 105 Processing sheet with id=AA3, first strand: chain 'A' and resid 112 through 113 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 120 Processing sheet with id=AA5, first strand: chain 'A' and resid 123 through 125 removed outlier: 6.951A pdb=" N ASP B 124 " --> pdb=" O ALA A 123 " (cutoff:3.500A) 17 hydrogen bonds defined for protein. 51 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: 0.12 Time building geometry restraints manager: 0.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 531 1.34 - 1.45: 99 1.45 - 1.57: 813 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 1449 Sorted by residual: bond pdb=" CB ASN C 139 " pdb=" CG ASN C 139 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.32e+00 bond pdb=" CB ASN A 139 " pdb=" CG ASN A 139 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.31e+00 bond pdb=" CB ASN B 139 " pdb=" CG ASN B 139 " ideal model delta sigma weight residual 1.516 1.487 0.029 2.50e-02 1.60e+03 1.30e+00 bond pdb=" C ASP C 101 " pdb=" N SER C 102 " ideal model delta sigma weight residual 1.328 1.319 0.010 1.23e-02 6.61e+03 6.21e-01 bond pdb=" CA ASP C 124 " pdb=" CB ASP C 124 " ideal model delta sigma weight residual 1.537 1.523 0.014 1.76e-02 3.23e+03 6.20e-01 ... (remaining 1444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 1798 1.18 - 2.37: 118 2.37 - 3.55: 24 3.55 - 4.73: 7 4.73 - 5.91: 3 Bond angle restraints: 1950 Sorted by residual: angle pdb=" N ILE A 149 " pdb=" CA ILE A 149 " pdb=" C ILE A 149 " ideal model delta sigma weight residual 109.34 115.25 -5.91 2.08e+00 2.31e-01 8.08e+00 angle pdb=" N ILE C 149 " pdb=" CA ILE C 149 " pdb=" C ILE C 149 " ideal model delta sigma weight residual 109.34 115.22 -5.88 2.08e+00 2.31e-01 7.99e+00 angle pdb=" N ILE B 149 " pdb=" CA ILE B 149 " pdb=" C ILE B 149 " ideal model delta sigma weight residual 109.34 115.21 -5.87 2.08e+00 2.31e-01 7.98e+00 angle pdb=" C ALA B 123 " pdb=" N ASP B 124 " pdb=" CA ASP B 124 " ideal model delta sigma weight residual 122.46 118.89 3.57 1.80e+00 3.09e-01 3.93e+00 angle pdb=" C VAL B 148 " pdb=" N ILE B 149 " pdb=" CA ILE B 149 " ideal model delta sigma weight residual 121.97 125.51 -3.54 1.80e+00 3.09e-01 3.87e+00 ... (remaining 1945 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.47: 651 8.47 - 16.94: 117 16.94 - 25.41: 67 25.41 - 33.88: 14 33.88 - 42.35: 15 Dihedral angle restraints: 864 sinusoidal: 312 harmonic: 552 Sorted by residual: dihedral pdb=" CA GLU B 100 " pdb=" C GLU B 100 " pdb=" N ASP B 101 " pdb=" CA ASP B 101 " ideal model delta harmonic sigma weight residual -180.00 -162.32 -17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLU A 100 " pdb=" C GLU A 100 " pdb=" N ASP A 101 " pdb=" CA ASP A 101 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA GLU C 100 " pdb=" C GLU C 100 " pdb=" N ASP C 101 " pdb=" CA ASP C 101 " ideal model delta harmonic sigma weight residual -180.00 -162.39 -17.61 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 861 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 127 0.031 - 0.061: 74 0.061 - 0.091: 15 0.091 - 0.122: 16 0.122 - 0.152: 5 Chirality restraints: 237 Sorted by residual: chirality pdb=" CB ILE C 112 " pdb=" CA ILE C 112 " pdb=" CG1 ILE C 112 " pdb=" CG2 ILE C 112 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CB ILE B 112 " pdb=" CA ILE B 112 " pdb=" CG1 ILE B 112 " pdb=" CG2 ILE B 112 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.65e-01 chirality pdb=" CB ILE A 112 " pdb=" CA ILE A 112 " pdb=" CG1 ILE A 112 " pdb=" CG2 ILE A 112 " both_signs ideal model delta sigma weight residual False 2.64 2.50 0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 234 not shown) Planarity restraints: 261 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 101 " 0.006 2.00e-02 2.50e+03 1.22e-02 1.50e+00 pdb=" C ASP B 101 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP B 101 " 0.008 2.00e-02 2.50e+03 pdb=" N SER B 102 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 101 " 0.006 2.00e-02 2.50e+03 1.21e-02 1.47e+00 pdb=" C ASP C 101 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP C 101 " 0.008 2.00e-02 2.50e+03 pdb=" N SER C 102 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 101 " 0.006 2.00e-02 2.50e+03 1.20e-02 1.45e+00 pdb=" C ASP A 101 " -0.021 2.00e-02 2.50e+03 pdb=" O ASP A 101 " 0.008 2.00e-02 2.50e+03 pdb=" N SER A 102 " 0.007 2.00e-02 2.50e+03 ... (remaining 258 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.90: 643 2.90 - 3.40: 1286 3.40 - 3.90: 2048 3.90 - 4.40: 2290 4.40 - 4.90: 4494 Nonbonded interactions: 10761 Sorted by model distance: nonbonded pdb=" OD1 ASP C 92 " pdb=" N GLY C 93 " model vdw 2.395 3.120 nonbonded pdb=" OD1 ASP A 92 " pdb=" N GLY A 93 " model vdw 2.395 3.120 nonbonded pdb=" OD1 ASP B 92 " pdb=" N GLY B 93 " model vdw 2.395 3.120 nonbonded pdb=" OG SER B 134 " pdb=" NH2 ARG C 143 " model vdw 2.455 3.120 nonbonded pdb=" N ASP C 101 " pdb=" OD1 ASP C 101 " model vdw 2.462 3.120 ... (remaining 10756 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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: 3.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 2.800 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 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 : 0.005 0.029 1449 Z= 0.260 Angle : 0.729 5.914 1950 Z= 0.409 Chirality : 0.048 0.152 237 Planarity : 0.002 0.012 261 Dihedral : 13.404 42.355 516 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.88 % Favored : 76.12 % Rotamer: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -6.37 (0.35), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.85 (0.26), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 115 HIS 0.003 0.002 HIS B 120 Details of bonding type rmsd covalent geometry : bond 0.00543 ( 1449) covalent geometry : angle 0.72936 ( 1950) hydrogen bonds : bond 0.19869 ( 17) hydrogen bonds : angle 7.97544 ( 51) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.032 Fit side-chains revert: symmetry clash REVERT: A 101 ASP cc_start: 0.8306 (p0) cc_final: 0.8079 (p0) REVERT: B 101 ASP cc_start: 0.8203 (p0) cc_final: 0.7857 (p0) REVERT: B 128 LYS cc_start: 0.7774 (mmmt) cc_final: 0.7354 (mmtm) REVERT: B 131 ASN cc_start: 0.8264 (t0) cc_final: 0.8061 (t0) REVERT: C 92 ASP cc_start: 0.7944 (t0) cc_final: 0.7717 (t0) REVERT: C 128 LYS cc_start: 0.7647 (mmmt) cc_final: 0.7267 (tptt) REVERT: C 131 ASN cc_start: 0.8702 (t0) cc_final: 0.8306 (t0) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0505 time to fit residues: 1.9987 Evaluate side-chains 32 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 ASN B 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.103658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.089801 restraints weight = 2313.856| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.61 r_work: 0.3472 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1449 Z= 0.118 Angle : 0.610 6.472 1950 Z= 0.318 Chirality : 0.047 0.123 237 Planarity : 0.002 0.008 261 Dihedral : 4.606 16.904 210 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.42 % Favored : 84.58 % Rotamer: Outliers : 3.85 % Allowed : 16.67 % Favored : 79.49 % 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: -5.50 (0.42), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.19 (0.32), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 115 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00252 ( 1449) covalent geometry : angle 0.60986 ( 1950) hydrogen bonds : bond 0.02797 ( 17) hydrogen bonds : angle 4.45895 ( 51) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 28 time to evaluate : 0.074 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8132 (mt) REVERT: A 143 ARG cc_start: 0.8725 (ttt180) cc_final: 0.6394 (mtm180) REVERT: B 112 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7806 (mt) REVERT: B 128 LYS cc_start: 0.8023 (mmmt) cc_final: 0.7602 (mmtp) REVERT: B 131 ASN cc_start: 0.8374 (t0) cc_final: 0.8142 (t0) REVERT: B 133 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8176 (mm-30) REVERT: C 112 ILE cc_start: 0.8293 (OUTLIER) cc_final: 0.7771 (mt) REVERT: C 128 LYS cc_start: 0.7987 (mmmt) cc_final: 0.7623 (tptt) REVERT: C 131 ASN cc_start: 0.8812 (t0) cc_final: 0.8416 (t0) outliers start: 6 outliers final: 2 residues processed: 30 average time/residue: 0.0601 time to fit residues: 1.9943 Evaluate side-chains 29 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 16 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.4006 ------------------------------------------------------------------------------- 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 = 0.3720 r_free = 0.3720 target = 0.103052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.088732 restraints weight = 2359.597| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.75 r_work: 0.3451 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3345 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 1449 Z= 0.163 Angle : 0.625 7.079 1950 Z= 0.332 Chirality : 0.047 0.123 237 Planarity : 0.002 0.010 261 Dihedral : 4.689 15.872 210 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.90 % Favored : 80.10 % Rotamer: Outliers : 6.41 % Allowed : 15.38 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -5.19 (0.47), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.95 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 143 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 1449) covalent geometry : angle 0.62493 ( 1950) hydrogen bonds : bond 0.02965 ( 17) hydrogen bonds : angle 4.27341 ( 51) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 22 time to evaluate : 0.037 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8766 (ttt180) cc_final: 0.6348 (mtm180) REVERT: B 128 LYS cc_start: 0.8102 (mmmt) cc_final: 0.7675 (mmtm) REVERT: B 131 ASN cc_start: 0.8345 (t0) cc_final: 0.8126 (t0) REVERT: B 133 GLU cc_start: 0.8396 (mm-30) cc_final: 0.8170 (mm-30) REVERT: C 128 LYS cc_start: 0.7904 (mmmt) cc_final: 0.7558 (tptt) REVERT: C 131 ASN cc_start: 0.8874 (t0) cc_final: 0.8502 (t0) outliers start: 10 outliers final: 5 residues processed: 27 average time/residue: 0.0494 time to fit residues: 1.4872 Evaluate side-chains 27 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 6 optimal weight: 0.0470 chunk 2 optimal weight: 3.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- 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 = 0.3734 r_free = 0.3734 target = 0.104173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.089848 restraints weight = 2387.060| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.82 r_work: 0.3464 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1449 Z= 0.140 Angle : 0.592 6.845 1950 Z= 0.318 Chirality : 0.047 0.120 237 Planarity : 0.002 0.012 261 Dihedral : 4.438 15.218 210 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % Rotamer: Outliers : 3.85 % Allowed : 16.03 % Favored : 80.13 % 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: -5.05 (0.47), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 143 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 1449) covalent geometry : angle 0.59231 ( 1950) hydrogen bonds : bond 0.02307 ( 17) hydrogen bonds : angle 4.20863 ( 51) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.055 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8733 (ttt180) cc_final: 0.6320 (mtm180) REVERT: B 128 LYS cc_start: 0.8104 (mmmt) cc_final: 0.7640 (mmtm) REVERT: B 131 ASN cc_start: 0.8299 (t0) cc_final: 0.8069 (t0) REVERT: B 133 GLU cc_start: 0.8346 (mm-30) cc_final: 0.8105 (mm-30) REVERT: C 128 LYS cc_start: 0.8018 (mmmt) cc_final: 0.7631 (tptt) REVERT: C 131 ASN cc_start: 0.8871 (t0) cc_final: 0.8454 (t0) outliers start: 6 outliers final: 4 residues processed: 23 average time/residue: 0.0957 time to fit residues: 2.4253 Evaluate side-chains 26 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 13 optimal weight: 0.0670 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.3770 r_free = 0.3770 target = 0.105893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.092160 restraints weight = 2302.938| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 2.69 r_work: 0.3510 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1449 Z= 0.105 Angle : 0.602 10.343 1950 Z= 0.300 Chirality : 0.047 0.126 237 Planarity : 0.002 0.010 261 Dihedral : 4.025 15.029 210 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.41 % Favored : 82.59 % Rotamer: Outliers : 3.21 % Allowed : 17.31 % Favored : 79.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.89 (0.49), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.72 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 143 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 1449) covalent geometry : angle 0.60200 ( 1950) hydrogen bonds : bond 0.01847 ( 17) hydrogen bonds : angle 4.09166 ( 51) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.052 Fit side-chains revert: symmetry clash REVERT: A 112 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8030 (mt) REVERT: A 143 ARG cc_start: 0.8715 (ttt180) cc_final: 0.6372 (mtm180) REVERT: B 128 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7668 (mmtm) REVERT: B 131 ASN cc_start: 0.8298 (t0) cc_final: 0.8075 (t0) REVERT: B 133 GLU cc_start: 0.8288 (mm-30) cc_final: 0.8051 (mm-30) REVERT: C 128 LYS cc_start: 0.7969 (mmmt) cc_final: 0.7615 (tptt) outliers start: 5 outliers final: 4 residues processed: 20 average time/residue: 0.1396 time to fit residues: 2.9949 Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 9.9990 chunk 11 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.102608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.088467 restraints weight = 2339.158| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 2.78 r_work: 0.3437 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3332 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 1449 Z= 0.201 Angle : 0.659 8.364 1950 Z= 0.349 Chirality : 0.048 0.122 237 Planarity : 0.003 0.019 261 Dihedral : 4.723 15.249 210 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.90 % Favored : 80.10 % Rotamer: Outliers : 3.85 % Allowed : 17.31 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -5.02 (0.48), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.82 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 HIS 0.003 0.002 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 1449) covalent geometry : angle 0.65936 ( 1950) hydrogen bonds : bond 0.02807 ( 17) hydrogen bonds : angle 4.24899 ( 51) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.060 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8797 (ttt180) cc_final: 0.6352 (mtm180) REVERT: B 128 LYS cc_start: 0.8179 (mmmt) cc_final: 0.7704 (mmtm) REVERT: B 131 ASN cc_start: 0.8317 (t0) cc_final: 0.8095 (t0) REVERT: C 92 ASP cc_start: 0.8018 (t0) cc_final: 0.7812 (t0) REVERT: C 128 LYS cc_start: 0.7959 (mmmt) cc_final: 0.7599 (tptt) REVERT: C 131 ASN cc_start: 0.8886 (t0) cc_final: 0.8506 (t0) outliers start: 6 outliers final: 5 residues processed: 23 average time/residue: 0.0949 time to fit residues: 2.3956 Evaluate side-chains 27 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 0.1980 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.103917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.090003 restraints weight = 2328.695| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 2.77 r_work: 0.3467 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 1449 Z= 0.142 Angle : 0.607 7.418 1950 Z= 0.316 Chirality : 0.047 0.120 237 Planarity : 0.002 0.011 261 Dihedral : 4.448 15.459 210 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.92 % Favored : 83.08 % Rotamer: Outliers : 3.21 % Allowed : 19.23 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.93 (0.48), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 1449) covalent geometry : angle 0.60678 ( 1950) hydrogen bonds : bond 0.02253 ( 17) hydrogen bonds : angle 4.15871 ( 51) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.058 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8749 (ttt180) cc_final: 0.6331 (mtm180) REVERT: B 128 LYS cc_start: 0.8152 (mmmt) cc_final: 0.7688 (mmtm) REVERT: B 131 ASN cc_start: 0.8266 (t0) cc_final: 0.8039 (t0) REVERT: C 92 ASP cc_start: 0.8002 (t0) cc_final: 0.7782 (t0) REVERT: C 128 LYS cc_start: 0.8022 (mmmt) cc_final: 0.7631 (tptt) REVERT: C 131 ASN cc_start: 0.8877 (t0) cc_final: 0.8479 (t0) outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.1065 time to fit residues: 2.4513 Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 6 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 14 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.3668 r_free = 0.3668 target = 0.100973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.086937 restraints weight = 2323.504| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.73 r_work: 0.3402 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1449 Z= 0.241 Angle : 0.696 7.080 1950 Z= 0.375 Chirality : 0.049 0.124 237 Planarity : 0.003 0.009 261 Dihedral : 5.190 17.246 210 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.39 % Favored : 78.61 % Rotamer: Outliers : 4.49 % Allowed : 17.95 % Favored : 77.56 % 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: -5.11 (0.47), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.89 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 HIS 0.004 0.002 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 1449) covalent geometry : angle 0.69603 ( 1950) hydrogen bonds : bond 0.03136 ( 17) hydrogen bonds : angle 4.28585 ( 51) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.053 Fit side-chains REVERT: A 128 LYS cc_start: 0.8135 (mmmt) cc_final: 0.7626 (mmtp) REVERT: A 143 ARG cc_start: 0.8796 (ttt180) cc_final: 0.6320 (mtm180) REVERT: B 128 LYS cc_start: 0.8125 (mmmt) cc_final: 0.7639 (mmtm) REVERT: B 131 ASN cc_start: 0.8313 (t0) cc_final: 0.8101 (t0) REVERT: C 128 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7632 (tptt) REVERT: C 131 ASN cc_start: 0.8905 (t0) cc_final: 0.8517 (t0) outliers start: 7 outliers final: 5 residues processed: 23 average time/residue: 0.0791 time to fit residues: 2.0411 Evaluate side-chains 26 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 21 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 11 optimal weight: 0.7980 chunk 10 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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 = 0.3667 r_free = 0.3667 target = 0.101005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.087024 restraints weight = 2341.408| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 2.77 r_work: 0.3401 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3298 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 1449 Z= 0.241 Angle : 0.747 8.338 1950 Z= 0.403 Chirality : 0.049 0.126 237 Planarity : 0.003 0.013 261 Dihedral : 5.189 16.939 210 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.90 % Favored : 80.10 % Rotamer: Outliers : 3.21 % Allowed : 19.23 % Favored : 77.56 % 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: -5.11 (0.47), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.36), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 HIS 0.004 0.002 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 1449) covalent geometry : angle 0.74737 ( 1950) hydrogen bonds : bond 0.03087 ( 17) hydrogen bonds : angle 4.23764 ( 51) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.070 Fit side-chains REVERT: A 128 LYS cc_start: 0.8107 (mmmt) cc_final: 0.7631 (mmtp) REVERT: B 128 LYS cc_start: 0.8091 (mmmt) cc_final: 0.7624 (mmtp) REVERT: B 131 ASN cc_start: 0.8316 (t0) cc_final: 0.8100 (t0) REVERT: C 128 LYS cc_start: 0.7995 (mmmt) cc_final: 0.7631 (tptt) REVERT: C 131 ASN cc_start: 0.8907 (t0) cc_final: 0.8506 (t0) outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.0622 time to fit residues: 1.5389 Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.104149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.090406 restraints weight = 2326.460| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.73 r_work: 0.3468 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3368 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 1449 Z= 0.158 Angle : 0.671 7.980 1950 Z= 0.360 Chirality : 0.048 0.121 237 Planarity : 0.002 0.011 261 Dihedral : 4.515 15.919 210 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.41 % Favored : 81.59 % Rotamer: Outliers : 3.21 % Allowed : 18.59 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.95 (0.48), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 HIS 0.002 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 1449) covalent geometry : angle 0.67131 ( 1950) hydrogen bonds : bond 0.02334 ( 17) hydrogen bonds : angle 4.13827 ( 51) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 402 Ramachandran restraints generated. 201 Oldfield, 0 Emsley, 201 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.073 Fit side-chains revert: symmetry clash REVERT: A 143 ARG cc_start: 0.8782 (ttt180) cc_final: 0.6353 (mtm180) REVERT: B 128 LYS cc_start: 0.8060 (mmmt) cc_final: 0.7650 (mmtm) REVERT: B 131 ASN cc_start: 0.8314 (t0) cc_final: 0.8090 (t0) REVERT: C 128 LYS cc_start: 0.8002 (mmmt) cc_final: 0.7638 (tptt) REVERT: C 131 ASN cc_start: 0.8863 (t0) cc_final: 0.8467 (t0) outliers start: 5 outliers final: 5 residues processed: 21 average time/residue: 0.1116 time to fit residues: 2.5709 Evaluate side-chains 25 residues out of total 156 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 20 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 88 THR Chi-restraints excluded: chain B residue 88 THR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 88 THR Chi-restraints excluded: chain C residue 112 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3731 r_free = 0.3731 target = 0.104120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.090159 restraints weight = 2333.401| |-----------------------------------------------------------------------------| r_work (start): 0.3563 rms_B_bonded: 2.77 r_work: 0.3468 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1449 Z= 0.157 Angle : 0.646 7.646 1950 Z= 0.344 Chirality : 0.047 0.119 237 Planarity : 0.002 0.015 261 Dihedral : 4.484 15.794 210 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.40 % Favored : 80.60 % Rotamer: Outliers : 3.21 % Allowed : 19.23 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.88 (0.49), residues: 201 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.37), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 HIS 0.002 0.001 HIS A 120 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 1449) covalent geometry : angle 0.64576 ( 1950) hydrogen bonds : bond 0.02377 ( 17) hydrogen bonds : angle 4.16418 ( 51) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 717.48 seconds wall clock time: 13 minutes 14.33 seconds (794.33 seconds total)