Starting phenix.real_space_refine on Thu Oct 22 19:17:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28iz_56538/10_2026/28iz_56538.cif Found real_map, /net/cci-nas-00/data/ceres_data/28iz_56538/10_2026/28iz_56538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/28iz_56538/10_2026/28iz_56538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28iz_56538/10_2026/28iz_56538.map" model { file = "/net/cci-nas-00/data/ceres_data/28iz_56538/10_2026/28iz_56538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28iz_56538/10_2026/28iz_56538.cif" } resolution = 2.83 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians K 4 8.98 5 S 32 5.16 5 C 2762 2.51 5 N 636 2.21 5 O 716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 4150 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 255} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 7, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "B" Number of atoms: 1968 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1968 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 4, 'TRANS': 255} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 5, 'GLU:plan': 7, 'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 69 Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 109 Unusual residues: {' K': 4, 'Y01': 3} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.01, per 1000 atoms: 0.24 Number of scatterers: 4150 At special positions: 0 Unit cell: (59.072, 82.368, 96.512, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 4 19.00 S 32 16.00 O 716 8.00 N 636 7.00 C 2762 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: 0.28 Conformation dependent library (CDL) restraints added in 86.7 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 964 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 85.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 2 through 52 removed outlier: 5.544A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ILE A 48 " --> pdb=" O GLU A 44 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N TYR A 52 " --> pdb=" O ILE A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 74 Proline residue: A 71 - end of helix removed outlier: 3.933A pdb=" N ALA A 74 " --> pdb=" O GLU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 removed outlier: 3.558A pdb=" N LEU A 116 " --> pdb=" O PHE A 112 " (cutoff:3.500A) Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 removed outlier: 3.517A pdb=" N MET A 159 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'A' and resid 248 through 260 removed outlier: 3.525A pdb=" N GLU A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA A 258 " --> pdb=" O GLU A 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 52 removed outlier: 5.544A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE B 48 " --> pdb=" O GLU B 44 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TYR B 52 " --> pdb=" O ILE B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 74 Proline residue: B 71 - end of helix removed outlier: 3.933A pdb=" N ALA B 74 " --> pdb=" O GLU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 removed outlier: 3.558A pdb=" N LEU B 116 " --> pdb=" O PHE B 112 " (cutoff:3.500A) Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 removed outlier: 3.517A pdb=" N MET B 159 " --> pdb=" O SER B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 248 through 260 removed outlier: 3.525A pdb=" N GLU B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA B 258 " --> pdb=" O GLU B 254 " (cutoff:3.500A) 338 hydrogen bonds defined for protein. 1008 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.51 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 679 1.33 - 1.45: 1121 1.45 - 1.57: 2404 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4252 Sorted by residual: bond pdb=" N VAL A 242 " pdb=" CA VAL A 242 " ideal model delta sigma weight residual 1.454 1.462 -0.008 1.19e-02 7.06e+03 4.01e-01 bond pdb=" C GLU A 70 " pdb=" O GLU A 70 " ideal model delta sigma weight residual 1.244 1.237 0.006 1.00e-02 1.00e+04 3.76e-01 bond pdb=" C GLU B 70 " pdb=" O GLU B 70 " ideal model delta sigma weight residual 1.244 1.237 0.006 1.00e-02 1.00e+04 3.62e-01 bond pdb=" N VAL B 242 " pdb=" CA VAL B 242 " ideal model delta sigma weight residual 1.454 1.461 -0.007 1.19e-02 7.06e+03 3.03e-01 bond pdb=" N GLU A 70 " pdb=" CA GLU A 70 " ideal model delta sigma weight residual 1.461 1.466 -0.005 9.20e-03 1.18e+04 2.54e-01 ... (remaining 4247 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.95: 5522 0.95 - 1.89: 242 1.89 - 2.84: 18 2.84 - 3.79: 10 3.79 - 4.73: 8 Bond angle restraints: 5800 Sorted by residual: angle pdb=" C THR A 92 " pdb=" N THR A 93 " pdb=" CA THR A 93 " ideal model delta sigma weight residual 122.08 125.24 -3.16 1.47e+00 4.63e-01 4.61e+00 angle pdb=" C THR B 92 " pdb=" N THR B 93 " pdb=" CA THR B 93 " ideal model delta sigma weight residual 122.08 125.19 -3.11 1.47e+00 4.63e-01 4.48e+00 angle pdb=" C THR A 198 " pdb=" N THR A 199 " pdb=" CA THR A 199 " ideal model delta sigma weight residual 122.19 125.10 -2.91 1.41e+00 5.03e-01 4.25e+00 angle pdb=" C THR B 198 " pdb=" N THR B 199 " pdb=" CA THR B 199 " ideal model delta sigma weight residual 122.19 125.05 -2.86 1.41e+00 5.03e-01 4.13e+00 angle pdb=" N ILE B 118 " pdb=" CA ILE B 118 " pdb=" C ILE B 118 " ideal model delta sigma weight residual 108.88 112.15 -3.27 2.16e+00 2.14e-01 2.29e+00 ... (remaining 5795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.07: 2576 17.07 - 34.14: 134 34.14 - 51.21: 24 51.21 - 68.29: 10 68.29 - 85.36: 4 Dihedral angle restraints: 2748 sinusoidal: 1240 harmonic: 1508 Sorted by residual: dihedral pdb=" CB GLU A 44 " pdb=" CG GLU A 44 " pdb=" CD GLU A 44 " pdb=" OE1 GLU A 44 " ideal model delta sinusoidal sigma weight residual 0.00 -85.36 85.36 1 3.00e+01 1.11e-03 9.80e+00 dihedral pdb=" CB GLU B 44 " pdb=" CG GLU B 44 " pdb=" CD GLU B 44 " pdb=" OE1 GLU B 44 " ideal model delta sinusoidal sigma weight residual 0.00 -85.29 85.29 1 3.00e+01 1.11e-03 9.79e+00 dihedral pdb=" CA TRP B 78 " pdb=" C TRP B 78 " pdb=" N LYS B 79 " pdb=" CA LYS B 79 " ideal model delta harmonic sigma weight residual 180.00 164.63 15.37 0 5.00e+00 4.00e-02 9.45e+00 ... (remaining 2745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 437 0.024 - 0.047: 133 0.047 - 0.071: 92 0.071 - 0.094: 8 0.094 - 0.118: 14 Chirality restraints: 684 Sorted by residual: chirality pdb=" CA THR A 199 " pdb=" N THR A 199 " pdb=" C THR A 199 " pdb=" CB THR A 199 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.46e-01 chirality pdb=" CA THR A 93 " pdb=" N THR A 93 " pdb=" C THR A 93 " pdb=" CB THR A 93 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.44e-01 chirality pdb=" CA THR B 93 " pdb=" N THR B 93 " pdb=" C THR B 93 " pdb=" CB THR B 93 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.41e-01 ... (remaining 681 not shown) Planarity restraints: 688 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 118 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 119 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 119 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 119 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 118 " 0.019 5.00e-02 4.00e+02 2.84e-02 1.29e+00 pdb=" N PRO B 119 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 119 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 119 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 76 " -0.003 2.00e-02 2.50e+03 5.24e-03 2.74e-01 pdb=" C VAL A 76 " 0.009 2.00e-02 2.50e+03 pdb=" O VAL A 76 " -0.003 2.00e-02 2.50e+03 pdb=" N GLN A 77 " -0.003 2.00e-02 2.50e+03 ... (remaining 685 not shown) Histogram of nonbonded interaction distances: 2.62 - 3.13: 3219 3.13 - 3.63: 5018 3.63 - 4.13: 6881 4.13 - 4.64: 11318 4.64 - 5.14: 13822 Nonbonded interactions: 40258 Sorted by model distance: nonbonded pdb=" O THR A 198 " pdb=" OG1 THR A 199 " model vdw 2.622 3.040 nonbonded pdb=" O THR B 198 " pdb=" OG1 THR B 199 " model vdw 2.622 3.040 nonbonded pdb=" CAL Y01 B 302 " pdb=" OAW Y01 B 302 " model vdw 2.629 2.752 nonbonded pdb=" CAL Y01 A 305 " pdb=" OAW Y01 A 305 " model vdw 2.629 2.752 nonbonded pdb=" O GLY B 95 " pdb=" K K A 304 " model vdw 2.636 2.850 ... (remaining 40253 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' and resid 1 through 260) selection = (chain 'B' and resid 1 through 260) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 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: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 4.510 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 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 : 0.002 0.018 4252 Z= 0.094 Angle : 0.460 4.734 5800 Z= 0.271 Chirality : 0.033 0.118 684 Planarity : 0.002 0.029 688 Dihedral : 11.444 85.357 1784 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.31 (0.30), residues: 516 helix: -0.82 (0.19), residues: 410 sheet: None (None), residues: 0 loop : -0.26 (0.60), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 137 TYR 0.008 0.001 TYR B 85 PHE 0.009 0.001 PHE A 26 TRP 0.009 0.001 TRP B 78 HIS 0.001 0.001 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00205 / 0.09 ( 4252) covalent geometry : angle 0.45969 / 0.27 ( 5800) hydrogen bonds : bond 0.21023 / 13.94 ( 338) hydrogen bonds : angle 7.22028 / 5.38 ( 1008) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.098 Fit side-chains REVERT: A 53 ASN cc_start: 0.7416 (t0) cc_final: 0.7120 (t0) REVERT: B 53 ASN cc_start: 0.7422 (t0) cc_final: 0.7125 (t0) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.7512 time to fit residues: 46.1783 Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [24, 48, 26, 2, 16, 32, 31, 25, 50, 19, 30] chunk 24 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 0.0020 chunk 2 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 50 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.093610 restraints weight = 4674.361| |-----------------------------------------------------------------------------| r_work (start): 0.3010 rms_B_bonded: 1.59 r_work: 0.2897 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2779 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4252 Z= 0.125 Angle : 0.463 4.830 5800 Z= 0.261 Chirality : 0.036 0.117 684 Planarity : 0.003 0.019 688 Dihedral : 6.371 55.154 986 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.51 % Allowed : 6.15 % Favored : 93.33 % 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: 2.39 (0.34), residues: 516 helix: 2.01 (0.22), residues: 418 sheet: None (None), residues: 0 loop : -0.25 (0.62), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 245 TYR 0.013 0.001 TYR A 113 PHE 0.014 0.001 PHE B 109 TRP 0.005 0.001 TRP B 78 HIS 0.001 0.000 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 4252) covalent geometry : angle 0.46340 / 0.26 ( 5800) hydrogen bonds : bond 0.04795 / 3.19 ( 338) hydrogen bonds : angle 3.60978 / 2.63 ( 1008) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.108 Fit side-chains REVERT: A 53 ASN cc_start: 0.7325 (t0) cc_final: 0.6990 (t0) REVERT: B 53 ASN cc_start: 0.7318 (t0) cc_final: 0.6986 (t0) outliers start: 2 outliers final: 0 residues processed: 54 average time/residue: 0.5229 time to fit residues: 29.2662 Evaluate side-chains 50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [46, 18, 51, 19, 25, 2, 37, 17, 21, 48, 29] chunk 46 optimal weight: 2.9990 chunk 18 optimal weight: 0.4980 chunk 51 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.130396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.091499 restraints weight = 4511.418| |-----------------------------------------------------------------------------| r_work (start): 0.2973 rms_B_bonded: 1.58 r_work: 0.2867 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4252 Z= 0.129 Angle : 0.458 4.994 5800 Z= 0.253 Chirality : 0.036 0.120 684 Planarity : 0.002 0.015 688 Dihedral : 6.421 59.061 986 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.51 % Allowed : 8.21 % Favored : 91.28 % 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: 3.54 (0.35), residues: 516 helix: 2.86 (0.23), residues: 420 sheet: None (None), residues: 0 loop : -0.15 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 245 TYR 0.014 0.001 TYR B 113 PHE 0.013 0.001 PHE B 109 TRP 0.004 0.001 TRP B 78 HIS 0.001 0.000 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 ( 4252) covalent geometry : angle 0.45821 / 0.25 ( 5800) hydrogen bonds : bond 0.04543 / 3.02 ( 338) hydrogen bonds : angle 3.29742 / 2.41 ( 1008) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.087 Fit side-chains REVERT: A 168 MET cc_start: 0.6570 (mmp) cc_final: 0.6238 (mmm) REVERT: B 168 MET cc_start: 0.6552 (mmp) cc_final: 0.6222 (mmm) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.5504 time to fit residues: 28.4974 Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain B residue 141 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [26, 36, 21, 49, 4, 23, 31, 0, 7, 9, 8] chunk 26 optimal weight: 0.0470 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 overall best weight: 0.7080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.131127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.091870 restraints weight = 4558.141| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.63 r_work: 0.2891 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2774 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4252 Z= 0.123 Angle : 0.450 5.841 5800 Z= 0.247 Chirality : 0.036 0.117 684 Planarity : 0.002 0.014 688 Dihedral : 6.302 55.704 986 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.51 % Allowed : 9.74 % Favored : 89.74 % 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: 3.97 (0.35), residues: 516 helix: 3.17 (0.23), residues: 420 sheet: None (None), residues: 0 loop : -0.06 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 245 TYR 0.014 0.001 TYR A 113 PHE 0.012 0.001 PHE B 109 TRP 0.005 0.001 TRP A 184 HIS 0.001 0.000 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 ( 4252) covalent geometry : angle 0.45019 / 0.25 ( 5800) hydrogen bonds : bond 0.04251 / 2.83 ( 338) hydrogen bonds : angle 3.23531 / 2.36 ( 1008) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.140 Fit side-chains REVERT: A 168 MET cc_start: 0.6593 (mmp) cc_final: 0.6262 (mmm) REVERT: B 168 MET cc_start: 0.6576 (mmp) cc_final: 0.6245 (mmm) outliers start: 2 outliers final: 4 residues processed: 54 average time/residue: 0.4765 time to fit residues: 26.7626 Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ILE Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 141 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [30, 38, 4, 42, 24, 41, 47, 3, 6, 10, 44] chunk 30 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.128597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.092056 restraints weight = 4623.220| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 1.40 r_work: 0.2802 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 4252 Z= 0.226 Angle : 0.552 6.424 5800 Z= 0.301 Chirality : 0.041 0.148 684 Planarity : 0.003 0.018 688 Dihedral : 6.539 54.464 986 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 1.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.54 % Allowed : 10.26 % Favored : 88.21 % 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 are not related in a simple way. whole: 3.52 (0.35), residues: 516 helix: 2.82 (0.23), residues: 420 sheet: None (None), residues: 0 loop : -0.00 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 245 TYR 0.013 0.002 TYR B 113 PHE 0.012 0.002 PHE B 223 TRP 0.002 0.001 TRP A 184 HIS 0.001 0.000 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00553 / 0.23 ( 4252) covalent geometry : angle 0.55173 / 0.30 ( 5800) hydrogen bonds : bond 0.05437 / 3.61 ( 338) hydrogen bonds : angle 3.44993 / 2.52 ( 1008) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.119 Fit side-chains REVERT: A 168 MET cc_start: 0.6943 (mmp) cc_final: 0.6615 (mmm) REVERT: A 180 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: B 168 MET cc_start: 0.6955 (mmp) cc_final: 0.6626 (mmm) REVERT: B 180 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7434 (mp10) outliers start: 6 outliers final: 4 residues processed: 58 average time/residue: 0.7591 time to fit residues: 45.1928 Evaluate side-chains 64 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 239 LEU Chi-restraints excluded: chain B residue 141 LYS Chi-restraints excluded: chain B residue 180 GLN Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [23, 16, 36, 40, 34, 49, 24, 45, 0, 13, 3] chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.131474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.094954 restraints weight = 4713.220| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 1.44 r_work: 0.2817 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4252 Z= 0.125 Angle : 0.456 5.526 5800 Z= 0.251 Chirality : 0.036 0.117 684 Planarity : 0.003 0.042 688 Dihedral : 6.382 55.154 986 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.03 % Allowed : 12.31 % Favored : 86.67 % 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: 4.03 (0.35), residues: 516 helix: 3.19 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.05 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 245 TYR 0.014 0.001 TYR A 113 PHE 0.012 0.001 PHE B 109 TRP 0.005 0.001 TRP A 184 HIS 0.001 0.000 HIS A 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 ( 4252) covalent geometry : angle 0.45644 / 0.25 ( 5800) hydrogen bonds : bond 0.04283 / 2.85 ( 338) hydrogen bonds : angle 3.21417 / 2.35 ( 1008) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.123 Fit side-chains REVERT: A 168 MET cc_start: 0.6704 (mmp) cc_final: 0.6353 (mmm) REVERT: B 168 MET cc_start: 0.6703 (mmp) cc_final: 0.6354 (mmm) outliers start: 4 outliers final: 2 residues processed: 50 average time/residue: 0.5244 time to fit residues: 27.2139 Evaluate side-chains 50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain B residue 141 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [3, 17, 34, 47, 24, 25, 42, 36, 44, 48, 19] chunk 3 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 48 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.131008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094437 restraints weight = 4735.061| |-----------------------------------------------------------------------------| r_work (start): 0.2922 rms_B_bonded: 1.44 r_work: 0.2807 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4252 Z= 0.137 Angle : 0.476 7.231 5800 Z= 0.258 Chirality : 0.037 0.120 684 Planarity : 0.003 0.038 688 Dihedral : 6.396 56.035 986 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 1.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.51 % Allowed : 14.36 % Favored : 85.13 % 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 are not related in a simple way. whole: 4.05 (0.35), residues: 516 helix: 3.21 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.06 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 245 TYR 0.014 0.001 TYR B 113 PHE 0.011 0.001 PHE A 223 TRP 0.004 0.001 TRP A 184 HIS 0.001 0.000 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 ( 4252) covalent geometry : angle 0.47633 / 0.26 ( 5800) hydrogen bonds : bond 0.04419 / 2.94 ( 338) hydrogen bonds : angle 3.21732 / 2.35 ( 1008) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.156 Fit side-chains REVERT: A 168 MET cc_start: 0.6707 (mmp) cc_final: 0.6405 (mmm) REVERT: B 168 MET cc_start: 0.6706 (mmp) cc_final: 0.6405 (mmm) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.5485 time to fit residues: 28.4027 Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain B residue 141 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [36, 31, 15, 41, 19, 37, 43, 38, 40, 22, 33] chunk 36 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 41 optimal weight: 0.0040 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 0.2980 chunk 43 optimal weight: 0.9980 chunk 38 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 0.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.135635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.099495 restraints weight = 4592.574| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.43 r_work: 0.2882 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2762 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2762 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4252 Z= 0.101 Angle : 0.441 7.504 5800 Z= 0.234 Chirality : 0.035 0.111 684 Planarity : 0.003 0.035 688 Dihedral : 6.287 57.074 986 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 1.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.51 % Allowed : 14.62 % Favored : 84.87 % 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: 4.42 (0.36), residues: 516 helix: 3.47 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.13 (0.62), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 245 TYR 0.013 0.001 TYR B 113 PHE 0.012 0.001 PHE B 109 TRP 0.007 0.001 TRP A 184 HIS 0.001 0.000 HIS A 98 Details of bonding type rmsd/Z covalent geometry : bond 0.00201 / 0.10 ( 4252) covalent geometry : angle 0.44146 / 0.23 ( 5800) hydrogen bonds : bond 0.03687 / 2.46 ( 338) hydrogen bonds : angle 3.08125 / 2.24 ( 1008) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.150 Fit side-chains REVERT: A 168 MET cc_start: 0.6657 (mmp) cc_final: 0.6338 (mmm) REVERT: B 168 MET cc_start: 0.6660 (mmp) cc_final: 0.6344 (mmm) outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.4993 time to fit residues: 25.9433 Evaluate side-chains 50 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 48 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain B residue 141 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [45, 19, 32, 26, 29, 9, 41, 2, 36, 43, 11] chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.2980 chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 2 optimal weight: 0.7980 chunk 36 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.132158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.093631 restraints weight = 4611.954| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 1.54 r_work: 0.2836 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4252 Z= 0.115 Angle : 0.453 7.451 5800 Z= 0.243 Chirality : 0.036 0.117 684 Planarity : 0.003 0.036 688 Dihedral : 6.268 57.439 986 Min Nonbonded Distance : 2.628 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.03 % Allowed : 13.59 % Favored : 85.38 % 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: 4.40 (0.35), residues: 516 helix: 3.44 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.22 (0.63), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 245 TYR 0.014 0.001 TYR A 113 PHE 0.012 0.001 PHE B 109 TRP 0.005 0.001 TRP A 184 HIS 0.000 0.000 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 ( 4252) covalent geometry : angle 0.45330 / 0.24 ( 5800) hydrogen bonds : bond 0.03992 / 2.66 ( 338) hydrogen bonds : angle 3.11562 / 2.27 ( 1008) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 54 time to evaluate : 0.147 Fit side-chains REVERT: A 168 MET cc_start: 0.6591 (mmp) cc_final: 0.6261 (mmm) REVERT: B 168 MET cc_start: 0.6592 (mmp) cc_final: 0.6263 (mmm) outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.4767 time to fit residues: 27.7655 Evaluate side-chains 54 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 52 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain B residue 141 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [27, 25, 34, 16, 3, 45, 26, 39, 20, 40, 19] chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 20 optimal weight: 0.0370 chunk 40 optimal weight: 0.5980 chunk 19 optimal weight: 0.4980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 240 ASN B 53 ASN B 240 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.134503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.098125 restraints weight = 4575.725| |-----------------------------------------------------------------------------| r_work (start): 0.3006 rms_B_bonded: 1.45 r_work: 0.2900 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 4252 Z= 0.111 Angle : 0.449 7.335 5800 Z= 0.242 Chirality : 0.035 0.120 684 Planarity : 0.003 0.035 688 Dihedral : 6.215 57.507 986 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.77 % Allowed : 14.87 % Favored : 84.36 % 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: 4.48 (0.35), residues: 516 helix: 3.50 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.26 (0.63), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 245 TYR 0.014 0.001 TYR A 113 PHE 0.012 0.001 PHE B 109 TRP 0.005 0.001 TRP A 184 HIS 0.000 0.000 HIS A 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 ( 4252) covalent geometry : angle 0.44890 / 0.24 ( 5800) hydrogen bonds : bond 0.03878 / 2.59 ( 338) hydrogen bonds : angle 3.08476 / 2.24 ( 1008) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.140 Fit side-chains REVERT: A 168 MET cc_start: 0.6740 (mmp) cc_final: 0.6424 (mmm) REVERT: B 137 ARG cc_start: 0.7875 (OUTLIER) cc_final: 0.7501 (ttt90) REVERT: B 168 MET cc_start: 0.6716 (mmp) cc_final: 0.6398 (mmm) outliers start: 3 outliers final: 2 residues processed: 51 average time/residue: 0.5368 time to fit residues: 28.3263 Evaluate side-chains 53 residues out of total 438 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 50 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 141 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: [15, 0, 44, 25, 39, 42, 29, 2, 33, 26, 14] chunk 15 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 25 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 33 optimal weight: 0.0070 chunk 26 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 240 ASN B 240 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.131910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.095341 restraints weight = 4688.810| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.43 r_work: 0.2811 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4252 Z= 0.140 Angle : 0.482 7.273 5800 Z= 0.261 Chirality : 0.037 0.128 684 Planarity : 0.003 0.036 688 Dihedral : 6.282 56.983 986 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 1.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.77 % Allowed : 14.87 % Favored : 84.36 % 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: 4.25 (0.35), residues: 516 helix: 3.33 (0.23), residues: 420 sheet: None (None), residues: 0 loop : 0.25 (0.63), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 245 TYR 0.014 0.001 TYR A 113 PHE 0.012 0.001 PHE B 223 TRP 0.003 0.001 TRP A 184 HIS 0.001 0.000 HIS B 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 4252) covalent geometry : angle 0.48240 / 0.26 ( 5800) hydrogen bonds : bond 0.04419 / 2.94 ( 338) hydrogen bonds : angle 3.18615 / 2.32 ( 1008) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1514.23 seconds wall clock time: 26 minutes 43.35 seconds (1603.35 seconds total)