Starting phenix.real_space_refine on Tue Feb 3 12:20:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iyd_60996/02_2026/9iyd_60996.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iyd_60996/02_2026/9iyd_60996.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.09 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iyd_60996/02_2026/9iyd_60996.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iyd_60996/02_2026/9iyd_60996.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iyd_60996/02_2026/9iyd_60996.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iyd_60996/02_2026/9iyd_60996.map" } resolution = 3.09 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= 0.002 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 903 2.51 5 N 270 2.21 5 O 330 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 1509 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 503 Classifications: {'peptide': 72} Link IDs: {'TRANS': 71} Restraints were copied for chains: B, C Time building chain proxies: 0.41, per 1000 atoms: 0.27 Number of scatterers: 1509 At special positions: 0 Unit cell: (65.52, 72.24, 32.76, 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 330 8.00 N 270 7.00 C 903 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: 0.12 Conformation dependent library (CDL) restraints added in 67.0 milliseconds 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 366 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 4 sheets defined 0.0% alpha, 6.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 93 removed outlier: 6.588A pdb=" N ASP A 92 " --> pdb=" O ALA B 93 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 92 " --> pdb=" O ALA C 93 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 116 through 118 removed outlier: 6.851A pdb=" N LEU A 117 " --> pdb=" O VAL B 118 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N LEU B 117 " --> pdb=" O VAL C 118 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 144 Processing sheet with id=AA4, first strand: chain 'A' and resid 150 through 151 removed outlier: 6.636A pdb=" N GLY A 150 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLY B 150 " --> pdb=" O ILE C 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 2 hydrogen bonds defined for protein. 6 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: 0.17 Time building geometry restraints manager: 0.17 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: 555 1.34 - 1.45: 127 1.45 - 1.57: 824 1.57 - 1.68: 0 1.68 - 1.80: 6 Bond restraints: 1512 Sorted by residual: bond pdb=" CA SER B 102 " pdb=" CB SER B 102 " ideal model delta sigma weight residual 1.534 1.515 0.019 1.60e-02 3.91e+03 1.44e+00 bond pdb=" CA SER C 102 " pdb=" CB SER C 102 " ideal model delta sigma weight residual 1.534 1.516 0.019 1.60e-02 3.91e+03 1.38e+00 bond pdb=" CA SER A 102 " pdb=" CB SER A 102 " ideal model delta sigma weight residual 1.534 1.516 0.018 1.60e-02 3.91e+03 1.33e+00 bond pdb=" CB ASP A 124 " pdb=" CG ASP A 124 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.06e+00 bond pdb=" CB ASP B 124 " pdb=" CG ASP B 124 " ideal model delta sigma weight residual 1.516 1.491 0.025 2.50e-02 1.60e+03 1.03e+00 ... (remaining 1507 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.75: 1903 1.75 - 3.50: 122 3.50 - 5.25: 6 5.25 - 7.00: 3 7.00 - 8.75: 3 Bond angle restraints: 2037 Sorted by residual: angle pdb=" CA LEU B 126 " pdb=" CB LEU B 126 " pdb=" CG LEU B 126 " ideal model delta sigma weight residual 116.30 125.05 -8.75 3.50e+00 8.16e-02 6.25e+00 angle pdb=" CA LEU A 126 " pdb=" CB LEU A 126 " pdb=" CG LEU A 126 " ideal model delta sigma weight residual 116.30 125.04 -8.74 3.50e+00 8.16e-02 6.24e+00 angle pdb=" CA LEU C 126 " pdb=" CB LEU C 126 " pdb=" CG LEU C 126 " ideal model delta sigma weight residual 116.30 125.04 -8.74 3.50e+00 8.16e-02 6.24e+00 angle pdb=" CA LYS A 122 " pdb=" CB LYS A 122 " pdb=" CG LYS A 122 " ideal model delta sigma weight residual 114.10 118.73 -4.63 2.00e+00 2.50e-01 5.35e+00 angle pdb=" CA LYS B 122 " pdb=" CB LYS B 122 " pdb=" CG LYS B 122 " ideal model delta sigma weight residual 114.10 118.72 -4.62 2.00e+00 2.50e-01 5.34e+00 ... (remaining 2032 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.86: 696 9.86 - 19.72: 129 19.72 - 29.57: 54 29.57 - 39.43: 18 39.43 - 49.29: 6 Dihedral angle restraints: 903 sinusoidal: 324 harmonic: 579 Sorted by residual: dihedral pdb=" CA GLU C 121 " pdb=" CB GLU C 121 " pdb=" CG GLU C 121 " pdb=" CD GLU C 121 " ideal model delta sinusoidal sigma weight residual 60.00 108.03 -48.03 3 1.50e+01 4.44e-03 8.58e+00 dihedral pdb=" CA GLU A 121 " pdb=" CB GLU A 121 " pdb=" CG GLU A 121 " pdb=" CD GLU A 121 " ideal model delta sinusoidal sigma weight residual 60.00 107.99 -47.99 3 1.50e+01 4.44e-03 8.57e+00 dihedral pdb=" CA GLU B 121 " pdb=" CB GLU B 121 " pdb=" CG GLU B 121 " pdb=" CD GLU B 121 " ideal model delta sinusoidal sigma weight residual 60.00 107.96 -47.96 3 1.50e+01 4.44e-03 8.57e+00 ... (remaining 900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 89 0.026 - 0.052: 79 0.052 - 0.077: 32 0.077 - 0.103: 31 0.103 - 0.129: 18 Chirality restraints: 249 Sorted by residual: chirality pdb=" CA VAL A 103 " pdb=" N VAL A 103 " pdb=" C VAL A 103 " pdb=" CB VAL A 103 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA VAL C 103 " pdb=" N VAL C 103 " pdb=" C VAL C 103 " pdb=" CB VAL C 103 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL C 94 " pdb=" N VAL C 94 " pdb=" C VAL C 94 " pdb=" CB VAL C 94 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.93e-01 ... (remaining 246 not shown) Planarity restraints: 273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP A 96 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C ASP A 96 " 0.018 2.00e-02 2.50e+03 pdb=" O ASP A 96 " -0.007 2.00e-02 2.50e+03 pdb=" N VAL A 97 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 96 " -0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C ASP C 96 " 0.018 2.00e-02 2.50e+03 pdb=" O ASP C 96 " -0.007 2.00e-02 2.50e+03 pdb=" N VAL C 97 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 85 " 0.005 2.00e-02 2.50e+03 1.04e-02 1.08e+00 pdb=" C GLY B 85 " -0.018 2.00e-02 2.50e+03 pdb=" O GLY B 85 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN B 86 " 0.006 2.00e-02 2.50e+03 ... (remaining 270 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 722 2.92 - 3.42: 1304 3.42 - 3.91: 2193 3.91 - 4.41: 2508 4.41 - 4.90: 4554 Nonbonded interactions: 11281 Sorted by model distance: nonbonded pdb=" OG SER B 102 " pdb=" N VAL B 103 " model vdw 2.429 3.120 nonbonded pdb=" OG SER A 102 " pdb=" N VAL A 103 " model vdw 2.429 3.120 nonbonded pdb=" OG SER C 102 " pdb=" N VAL C 103 " model vdw 2.430 3.120 nonbonded pdb=" OD1 ASP B 124 " pdb=" O ASP C 124 " model vdw 2.458 3.040 nonbonded pdb=" N ASP C 109 " pdb=" OD1 ASP C 109 " model vdw 2.554 3.120 ... (remaining 11276 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: 2.480 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: 0.030 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.890 Find NCS groups from input model: 0.020 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:1.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 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 : 0.008 0.032 1512 Z= 0.402 Angle : 0.935 8.750 2037 Z= 0.490 Chirality : 0.054 0.129 249 Planarity : 0.004 0.010 273 Dihedral : 14.021 49.291 537 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 15.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.29 % Favored : 65.71 % Rotamer: Outliers : 0.00 % Allowed : 12.96 % Favored : 87.04 % 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 are not related in a simple way. whole: -7.05 (0.25), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -5.37 (0.19), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG C 143 HIS 0.004 0.002 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00836 ( 1512) covalent geometry : angle 0.93532 ( 2037) hydrogen bonds : bond 0.07589 ( 2) hydrogen bonds : angle 7.58953 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.067 Fit side-chains REVERT: A 91 LYS cc_start: 0.5599 (mmtp) cc_final: 0.5179 (mtmt) REVERT: B 91 LYS cc_start: 0.6221 (mmtp) cc_final: 0.5492 (mtmt) REVERT: C 91 LYS cc_start: 0.5930 (mmtp) cc_final: 0.5426 (mtmt) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.0519 time to fit residues: 1.7398 Evaluate side-chains 26 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 12 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN A 139 ASN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 131 ASN B 139 ASN ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 131 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.127009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.109879 restraints weight = 2064.630| |-----------------------------------------------------------------------------| r_work (start): 0.3719 rms_B_bonded: 2.56 r_work: 0.3644 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 1512 Z= 0.141 Angle : 0.596 5.989 2037 Z= 0.304 Chirality : 0.048 0.127 249 Planarity : 0.003 0.014 273 Dihedral : 4.309 12.084 219 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 0.62 % Allowed : 27.16 % Favored : 72.22 % 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 are not related in a simple way. whole: -6.34 (0.30), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.82 (0.23), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 115 HIS 0.002 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 1512) covalent geometry : angle 0.59627 ( 2037) hydrogen bonds : bond 0.02166 ( 2) hydrogen bonds : angle 7.69723 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.058 Fit side-chains REVERT: A 91 LYS cc_start: 0.5085 (mmtp) cc_final: 0.4732 (mtmt) REVERT: C 109 ASP cc_start: 0.7866 (p0) cc_final: 0.5771 (t0) outliers start: 1 outliers final: 1 residues processed: 25 average time/residue: 0.0386 time to fit residues: 1.2079 Evaluate side-chains 25 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 8 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 20 optimal weight: 0.0570 chunk 18 optimal weight: 0.6980 chunk 3 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.129114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.111650 restraints weight = 2071.560| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.61 r_work: 0.3669 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1512 Z= 0.116 Angle : 0.537 5.747 2037 Z= 0.274 Chirality : 0.047 0.124 249 Planarity : 0.002 0.011 273 Dihedral : 3.960 10.514 219 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.24 % Favored : 84.76 % Rotamer: Outliers : 2.47 % Allowed : 30.25 % Favored : 67.28 % 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 are not related in a simple way. whole: -6.02 (0.31), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.58 (0.24), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 115 HIS 0.002 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 1512) covalent geometry : angle 0.53682 ( 2037) hydrogen bonds : bond 0.01752 ( 2) hydrogen bonds : angle 7.55770 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.056 Fit side-chains REVERT: A 121 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8643 (mt-10) REVERT: B 121 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8260 (mt-10) REVERT: C 109 ASP cc_start: 0.7880 (p0) cc_final: 0.5708 (t0) REVERT: C 121 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.7950 (mt-10) outliers start: 4 outliers final: 1 residues processed: 23 average time/residue: 0.0421 time to fit residues: 1.1976 Evaluate side-chains 25 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 21 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain C residue 121 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 0.0000 chunk 13 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 chunk 18 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 139 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.131742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.114191 restraints weight = 2051.631| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.60 r_work: 0.3712 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1512 Z= 0.100 Angle : 0.499 4.942 2037 Z= 0.258 Chirality : 0.046 0.123 249 Planarity : 0.002 0.010 273 Dihedral : 3.730 9.933 219 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.52 % Favored : 90.48 % Rotamer: Outliers : 3.09 % Allowed : 29.63 % Favored : 67.28 % 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 are not related in a simple way. whole: -5.82 (0.33), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.43 (0.25), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 115 HIS 0.001 0.001 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 1512) covalent geometry : angle 0.49910 ( 2037) hydrogen bonds : bond 0.01550 ( 2) hydrogen bonds : angle 7.04048 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.075 Fit side-chains REVERT: A 121 GLU cc_start: 0.8907 (OUTLIER) cc_final: 0.8600 (mt-10) REVERT: B 121 GLU cc_start: 0.8999 (OUTLIER) cc_final: 0.8216 (mt-10) REVERT: C 109 ASP cc_start: 0.7869 (p0) cc_final: 0.5600 (t0) REVERT: C 121 GLU cc_start: 0.9013 (OUTLIER) cc_final: 0.7908 (mt-10) outliers start: 5 outliers final: 2 residues processed: 24 average time/residue: 0.0398 time to fit residues: 1.2452 Evaluate side-chains 27 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain C residue 121 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 13 optimal weight: 7.9990 chunk 15 optimal weight: 0.0270 chunk 12 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 overall best weight: 0.7642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.132143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.114536 restraints weight = 2046.719| |-----------------------------------------------------------------------------| r_work (start): 0.3790 rms_B_bonded: 2.61 r_work: 0.3716 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 1512 Z= 0.101 Angle : 0.488 4.643 2037 Z= 0.256 Chirality : 0.046 0.123 249 Planarity : 0.002 0.009 273 Dihedral : 3.653 9.866 219 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.43 % Favored : 88.57 % Rotamer: Outliers : 3.09 % Allowed : 30.25 % Favored : 66.67 % 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 are not related in a simple way. whole: -5.63 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.28 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 115 HIS 0.001 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 1512) covalent geometry : angle 0.48834 ( 2037) hydrogen bonds : bond 0.01450 ( 2) hydrogen bonds : angle 6.81848 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.066 Fit side-chains REVERT: A 121 GLU cc_start: 0.8885 (OUTLIER) cc_final: 0.8578 (mt-10) REVERT: B 121 GLU cc_start: 0.8998 (OUTLIER) cc_final: 0.8215 (mt-10) REVERT: C 109 ASP cc_start: 0.7871 (p0) cc_final: 0.5577 (t0) REVERT: C 121 GLU cc_start: 0.9011 (OUTLIER) cc_final: 0.7923 (mt-10) outliers start: 5 outliers final: 1 residues processed: 24 average time/residue: 0.0336 time to fit residues: 1.0530 Evaluate side-chains 26 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 22 time to evaluate : 0.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 126 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 4 optimal weight: 0.9980 chunk 1 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 2.9990 chunk 16 optimal weight: 0.0370 chunk 18 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 1.2062 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.129841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.112548 restraints weight = 2070.517| |-----------------------------------------------------------------------------| r_work (start): 0.3764 rms_B_bonded: 2.63 r_work: 0.3690 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3581 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 1512 Z= 0.133 Angle : 0.533 5.001 2037 Z= 0.278 Chirality : 0.046 0.122 249 Planarity : 0.002 0.019 273 Dihedral : 3.797 8.712 219 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 5.56 % Allowed : 27.16 % Favored : 67.28 % 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 are not related in a simple way. whole: -5.54 (0.35), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.22 (0.27), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 115 HIS 0.002 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 1512) covalent geometry : angle 0.53260 ( 2037) hydrogen bonds : bond 0.02142 ( 2) hydrogen bonds : angle 6.50397 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.058 Fit side-chains REVERT: A 121 GLU cc_start: 0.8958 (OUTLIER) cc_final: 0.8627 (mt-10) REVERT: B 121 GLU cc_start: 0.9044 (OUTLIER) cc_final: 0.8281 (mt-10) REVERT: C 121 GLU cc_start: 0.9016 (OUTLIER) cc_final: 0.7935 (mt-10) outliers start: 9 outliers final: 3 residues processed: 26 average time/residue: 0.0235 time to fit residues: 0.8072 Evaluate side-chains 28 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 22 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 126 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 8.9990 chunk 14 optimal weight: 0.0000 chunk 9 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.129616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.112477 restraints weight = 2044.454| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 2.57 r_work: 0.3687 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1512 Z= 0.135 Angle : 0.563 5.292 2037 Z= 0.288 Chirality : 0.048 0.203 249 Planarity : 0.002 0.022 273 Dihedral : 3.835 9.257 219 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.38 % Favored : 87.62 % Rotamer: Outliers : 4.94 % Allowed : 28.40 % Favored : 66.67 % 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 are not related in a simple way. whole: -5.49 (0.36), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.27), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 115 HIS 0.002 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 1512) covalent geometry : angle 0.56273 ( 2037) hydrogen bonds : bond 0.01968 ( 2) hydrogen bonds : angle 6.30463 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 23 time to evaluate : 0.063 Fit side-chains REVERT: A 121 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8606 (mt-10) REVERT: B 84 LEU cc_start: 0.7962 (OUTLIER) cc_final: 0.7759 (tt) REVERT: B 121 GLU cc_start: 0.9031 (OUTLIER) cc_final: 0.8239 (mt-10) REVERT: C 121 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.7914 (mt-10) outliers start: 8 outliers final: 3 residues processed: 26 average time/residue: 0.0315 time to fit residues: 1.0728 Evaluate side-chains 29 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 84 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 126 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 5 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 5.9990 chunk 7 optimal weight: 0.0970 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 0 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.132461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.114956 restraints weight = 2027.321| |-----------------------------------------------------------------------------| r_work (start): 0.3805 rms_B_bonded: 2.61 r_work: 0.3733 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3624 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 1512 Z= 0.114 Angle : 0.565 6.308 2037 Z= 0.289 Chirality : 0.047 0.181 249 Planarity : 0.002 0.013 273 Dihedral : 3.654 8.977 219 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 6.79 % Allowed : 27.16 % Favored : 66.05 % 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 are not related in a simple way. whole: -5.37 (0.37), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.09 (0.28), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 143 HIS 0.001 0.001 HIS B 110 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 1512) covalent geometry : angle 0.56518 ( 2037) hydrogen bonds : bond 0.01697 ( 2) hydrogen bonds : angle 6.24765 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 21 time to evaluate : 0.063 Fit side-chains REVERT: A 121 GLU cc_start: 0.8895 (OUTLIER) cc_final: 0.8589 (mt-10) REVERT: B 121 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: C 121 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.7891 (mt-10) outliers start: 11 outliers final: 6 residues processed: 26 average time/residue: 0.0301 time to fit residues: 1.0274 Evaluate side-chains 29 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 20 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 121 GLU Chi-restraints excluded: chain C residue 126 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 15 optimal weight: 0.0020 chunk 3 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.128967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.111495 restraints weight = 2070.471| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 2.60 r_work: 0.3676 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3567 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 1512 Z= 0.167 Angle : 0.655 9.354 2037 Z= 0.325 Chirality : 0.049 0.229 249 Planarity : 0.003 0.026 273 Dihedral : 3.932 9.425 219 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 4.94 % Allowed : 28.40 % Favored : 66.67 % 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 are not related in a simple way. whole: -5.42 (0.37), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.28), residues: 210 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 0.00355 ( 1512) covalent geometry : angle 0.65471 ( 2037) hydrogen bonds : bond 0.02413 ( 2) hydrogen bonds : angle 6.22369 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.037 Fit side-chains REVERT: A 121 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8610 (mt-10) REVERT: B 121 GLU cc_start: 0.9038 (OUTLIER) cc_final: 0.8302 (mt-10) REVERT: C 121 GLU cc_start: 0.9020 (OUTLIER) cc_final: 0.7916 (mt-10) outliers start: 8 outliers final: 5 residues processed: 23 average time/residue: 0.0200 time to fit residues: 0.6068 Evaluate side-chains 28 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 20 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 5 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN C 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.125225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.108253 restraints weight = 2048.696| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.51 r_work: 0.3614 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 1512 Z= 0.285 Angle : 0.788 8.057 2037 Z= 0.401 Chirality : 0.052 0.229 249 Planarity : 0.003 0.014 273 Dihedral : 4.708 12.799 219 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.33 % Favored : 76.67 % Rotamer: Outliers : 4.94 % Allowed : 29.01 % Favored : 66.05 % 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 are not related in a simple way. whole: -5.73 (0.34), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.36 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 143 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00604 ( 1512) covalent geometry : angle 0.78823 ( 2037) hydrogen bonds : bond 0.03680 ( 2) hydrogen bonds : angle 6.42648 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 420 Ramachandran restraints generated. 210 Oldfield, 0 Emsley, 210 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 21 time to evaluate : 0.061 Fit side-chains REVERT: A 91 LYS cc_start: 0.5151 (mmtp) cc_final: 0.4861 (mtmt) REVERT: A 121 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8596 (mt-10) REVERT: B 121 GLU cc_start: 0.9139 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: C 121 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.7963 (mt-10) outliers start: 8 outliers final: 4 residues processed: 25 average time/residue: 0.0326 time to fit residues: 1.0073 Evaluate side-chains 28 residues out of total 162 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 21 time to evaluate : 0.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ASN Chi-restraints excluded: chain A residue 101 ASP Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain C residue 86 ASN Chi-restraints excluded: chain C residue 121 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 11 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.125247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.108260 restraints weight = 2038.157| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 2.51 r_work: 0.3614 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.027 1512 Z= 0.263 Angle : 0.754 7.771 2037 Z= 0.386 Chirality : 0.051 0.190 249 Planarity : 0.003 0.014 273 Dihedral : 4.687 12.631 219 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.38 % Favored : 77.62 % Rotamer: Outliers : 4.94 % Allowed : 30.25 % Favored : 64.81 % 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 are not related in a simple way. whole: -5.78 (0.33), residues: 210 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.40 (0.26), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 143 HIS 0.003 0.001 HIS A 110 Details of bonding type rmsd covalent geometry : bond 0.00556 ( 1512) covalent geometry : angle 0.75426 ( 2037) hydrogen bonds : bond 0.03204 ( 2) hydrogen bonds : angle 6.65627 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 732.42 seconds wall clock time: 13 minutes 22.01 seconds (802.01 seconds total)