Starting phenix.real_space_refine on Wed Sep 17 04:46:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7w_61212/09_2025/9j7w_61212.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7w_61212/09_2025/9j7w_61212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j7w_61212/09_2025/9j7w_61212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7w_61212/09_2025/9j7w_61212.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7w_61212/09_2025/9j7w_61212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7w_61212/09_2025/9j7w_61212.cif" } resolution = 2.69 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= 0.007 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 P 2 5.49 5 S 40 5.16 5 C 2920 2.51 5 N 692 2.21 5 O 796 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4450 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2155 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 265, 2144 Classifications: {'peptide': 265} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 257} Conformer: "B" Number of residues, atoms: 265, 2144 Classifications: {'peptide': 265} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 257} bond proxies already assigned to first conformer: 2206 Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 52 Unusual residues: {'PC1': 1, 'RET': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'RET:plan-5': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "C" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Restraints were copied for chains: C Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N AARG A 287 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 287 " occ=0.50 residue: pdb=" N AARG C 287 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 287 " occ=0.50 Time building chain proxies: 1.94, per 1000 atoms: 0.44 Number of scatterers: 4450 At special positions: 0 Unit cell: (72.21, 70.55, 91.3, 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) S 40 16.00 P 2 15.00 O 796 8.00 N 692 7.00 C 2920 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 342.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 984 Finding SS restraints... Secondary structure from input PDB file: 22 helices and 2 sheets defined 75.1% alpha, 2.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 43 through 71 Processing helix chain 'A' and resid 72 through 74 No H-bonds generated for 'chain 'A' and resid 72 through 74' Processing helix chain 'A' and resid 77 through 97 removed outlier: 3.594A pdb=" N ILE A 81 " --> pdb=" O GLY A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 135 Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 144 through 167 removed outlier: 3.678A pdb=" N MET A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 201 Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 205 through 221 Processing helix chain 'A' and resid 221 through 230 removed outlier: 3.975A pdb=" N CYS A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 254 Processing helix chain 'A' and resid 254 through 275 Processing helix chain 'C' and resid 43 through 71 Processing helix chain 'C' and resid 72 through 74 No H-bonds generated for 'chain 'C' and resid 72 through 74' Processing helix chain 'C' and resid 77 through 97 removed outlier: 3.594A pdb=" N ILE C 81 " --> pdb=" O GLY C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 135 Proline residue: C 127 - end of helix Processing helix chain 'C' and resid 144 through 167 removed outlier: 3.678A pdb=" N MET C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 201 Processing helix chain 'C' and resid 202 through 204 No H-bonds generated for 'chain 'C' and resid 202 through 204' Processing helix chain 'C' and resid 205 through 221 Processing helix chain 'C' and resid 221 through 230 removed outlier: 3.975A pdb=" N CYS C 225 " --> pdb=" O LEU C 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 254 Processing helix chain 'C' and resid 254 through 275 Processing sheet with id=AA1, first strand: chain 'A' and resid 104 through 107 Processing sheet with id=AA2, first strand: chain 'C' and resid 104 through 107 310 hydrogen bonds defined for protein. 924 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: 0.62 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 730 1.33 - 1.45: 1412 1.45 - 1.57: 2360 1.57 - 1.69: 4 1.69 - 1.81: 56 Bond restraints: 4562 Sorted by residual: bond pdb=" C14 RET A 302 " pdb=" C15 RET A 302 " ideal model delta sigma weight residual 1.448 1.385 0.063 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C14 RET C 302 " pdb=" C15 RET C 302 " ideal model delta sigma weight residual 1.448 1.385 0.063 2.00e-02 2.50e+03 9.86e+00 bond pdb=" C8 RET A 302 " pdb=" C9 RET A 302 " ideal model delta sigma weight residual 1.450 1.389 0.061 2.00e-02 2.50e+03 9.30e+00 bond pdb=" C8 RET C 302 " pdb=" C9 RET C 302 " ideal model delta sigma weight residual 1.450 1.390 0.060 2.00e-02 2.50e+03 8.99e+00 bond pdb=" C10 RET A 302 " pdb=" C11 RET A 302 " ideal model delta sigma weight residual 1.433 1.379 0.054 2.00e-02 2.50e+03 7.35e+00 ... (remaining 4557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.12: 5790 1.12 - 2.25: 327 2.25 - 3.37: 56 3.37 - 4.49: 19 4.49 - 5.62: 8 Bond angle restraints: 6200 Sorted by residual: angle pdb=" CA GLY C 235 " pdb=" C GLY C 235 " pdb=" N ASN C 236 " ideal model delta sigma weight residual 114.65 117.04 -2.39 9.20e-01 1.18e+00 6.77e+00 angle pdb=" CA GLY A 235 " pdb=" C GLY A 235 " pdb=" N ASN A 236 " ideal model delta sigma weight residual 114.65 117.03 -2.38 9.20e-01 1.18e+00 6.71e+00 angle pdb=" C PHE A 96 " pdb=" N TRP A 97 " pdb=" CA TRP A 97 " ideal model delta sigma weight residual 122.59 120.24 2.35 1.11e+00 8.12e-01 4.48e+00 angle pdb=" C PHE C 96 " pdb=" N TRP C 97 " pdb=" CA TRP C 97 " ideal model delta sigma weight residual 122.59 120.24 2.35 1.11e+00 8.12e-01 4.47e+00 angle pdb=" N PHE A 85 " pdb=" CA PHE A 85 " pdb=" CB PHE A 85 " ideal model delta sigma weight residual 110.01 107.08 2.93 1.45e+00 4.76e-01 4.08e+00 ... (remaining 6195 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.47: 2323 16.47 - 32.93: 185 32.93 - 49.40: 52 49.40 - 65.87: 4 65.87 - 82.34: 6 Dihedral angle restraints: 2570 sinusoidal: 1014 harmonic: 1556 Sorted by residual: dihedral pdb=" CA SER C 231 " pdb=" C SER C 231 " pdb=" N GLU C 232 " pdb=" CA GLU C 232 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER A 231 " pdb=" C SER A 231 " pdb=" N GLU A 232 " pdb=" CA GLU A 232 " ideal model delta harmonic sigma weight residual 180.00 159.60 20.40 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA ILE A 107 " pdb=" C ILE A 107 " pdb=" N TYR A 108 " pdb=" CA TYR A 108 " ideal model delta harmonic sigma weight residual -180.00 -160.08 -19.92 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 2567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 339 0.025 - 0.049: 153 0.049 - 0.074: 101 0.074 - 0.099: 27 0.099 - 0.123: 8 Chirality restraints: 628 Sorted by residual: chirality pdb=" CB THR C 153 " pdb=" CA THR C 153 " pdb=" OG1 THR C 153 " pdb=" CG2 THR C 153 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL A 114 " pdb=" N VAL A 114 " pdb=" C VAL A 114 " pdb=" CB VAL A 114 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA VAL C 114 " pdb=" N VAL C 114 " pdb=" C VAL C 114 " pdb=" CB VAL C 114 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.65e-01 ... (remaining 625 not shown) Planarity restraints: 760 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C12 RET A 302 " -0.040 2.00e-02 2.50e+03 4.61e-02 2.65e+01 pdb=" C13 RET A 302 " 0.011 2.00e-02 2.50e+03 pdb=" C14 RET A 302 " 0.075 2.00e-02 2.50e+03 pdb=" C15 RET A 302 " -0.056 2.00e-02 2.50e+03 pdb=" C20 RET A 302 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 RET C 302 " 0.040 2.00e-02 2.50e+03 4.59e-02 2.63e+01 pdb=" C13 RET C 302 " -0.012 2.00e-02 2.50e+03 pdb=" C14 RET C 302 " -0.075 2.00e-02 2.50e+03 pdb=" C15 RET C 302 " 0.056 2.00e-02 2.50e+03 pdb=" C20 RET C 302 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 85 " 0.016 2.00e-02 2.50e+03 1.23e-02 2.65e+00 pdb=" CG PHE A 85 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE A 85 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 85 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 85 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 85 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 85 " 0.007 2.00e-02 2.50e+03 ... (remaining 757 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.55: 42 2.55 - 3.14: 3670 3.14 - 3.73: 7269 3.73 - 4.31: 10131 4.31 - 4.90: 16735 Nonbonded interactions: 37847 Sorted by model distance: nonbonded pdb=" OG SER A 137 " pdb=" OE1 GLU A 139 " model vdw 1.965 3.040 nonbonded pdb=" OG SER C 137 " pdb=" OE1 GLU C 139 " model vdw 1.966 3.040 nonbonded pdb=" OH TYR C 49 " pdb=" O HOH C 401 " model vdw 2.051 3.040 nonbonded pdb=" OH TYR A 49 " pdb=" O HOH A 401 " model vdw 2.052 3.040 nonbonded pdb=" O HOH A 402 " pdb=" O HOH A 412 " model vdw 2.054 3.040 ... (remaining 37842 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 '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=0.50 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: 1.390 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: 0.010 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.920 Find NCS groups from input model: 0.030 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:6.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 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 : 0.006 0.097 4564 Z= 0.315 Angle : 0.639 5.616 6200 Z= 0.363 Chirality : 0.038 0.123 628 Planarity : 0.005 0.046 760 Dihedral : 13.618 82.335 1586 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.86 (0.37), residues: 532 helix: 2.29 (0.27), residues: 366 sheet: None (None), residues: 0 loop : -1.29 (0.46), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 265 TYR 0.013 0.001 TYR A 182 PHE 0.027 0.002 PHE C 85 TRP 0.009 0.001 TRP C 116 HIS 0.006 0.001 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 4562) covalent geometry : angle 0.63863 ( 6200) hydrogen bonds : bond 0.10417 ( 310) hydrogen bonds : angle 5.22509 ( 924) Misc. bond : bond 0.09589 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.180 Fit side-chains REVERT: A 274 THR cc_start: 0.8386 (m) cc_final: 0.8180 (p) REVERT: C 274 THR cc_start: 0.8377 (m) cc_final: 0.8162 (p) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.6839 time to fit residues: 73.1120 Evaluate side-chains 70 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 104 GLN A 106 ASN A 145 HIS A 255 ASN C 41 HIS C 104 GLN C 106 ASN C 145 HIS C 255 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.091338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.067645 restraints weight = 27259.614| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 4.42 r_work: 0.2770 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2758 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2758 r_free = 0.2758 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2758 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4564 Z= 0.151 Angle : 0.625 11.276 6200 Z= 0.329 Chirality : 0.039 0.174 628 Planarity : 0.003 0.030 760 Dihedral : 9.776 81.542 658 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.25 % Allowed : 11.71 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.36), residues: 532 helix: 2.64 (0.25), residues: 384 sheet: None (None), residues: 0 loop : -0.62 (0.54), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.022 0.001 TYR C 49 PHE 0.008 0.001 PHE C 64 TRP 0.008 0.001 TRP C 211 HIS 0.002 0.001 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00337 ( 4562) covalent geometry : angle 0.62484 ( 6200) hydrogen bonds : bond 0.04416 ( 310) hydrogen bonds : angle 3.65108 ( 924) Misc. bond : bond 0.00076 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 MET cc_start: 0.7399 (tmm) cc_final: 0.7143 (tpt) REVERT: C 104 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8597 (tt0) REVERT: C 290 MET cc_start: 0.7388 (tmm) cc_final: 0.7133 (tpt) outliers start: 10 outliers final: 1 residues processed: 92 average time/residue: 0.6893 time to fit residues: 65.2543 Evaluate side-chains 73 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Chi-restraints excluded: chain C residue 104 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.0670 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 35 optimal weight: 0.6980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 104 GLN C 41 HIS C 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.093884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.070891 restraints weight = 26261.278| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 4.21 r_work: 0.2763 rms_B_bonded: 4.48 restraints_weight: 0.5000 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2763 r_free = 0.2763 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4564 Z= 0.135 Angle : 0.573 7.026 6200 Z= 0.304 Chirality : 0.038 0.159 628 Planarity : 0.003 0.028 760 Dihedral : 9.455 81.955 658 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.13 % Allowed : 16.44 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.92 (0.36), residues: 532 helix: 2.82 (0.24), residues: 384 sheet: None (None), residues: 0 loop : -0.55 (0.55), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.016 0.001 TYR C 49 PHE 0.008 0.001 PHE A 85 TRP 0.009 0.001 TRP A 211 HIS 0.002 0.001 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 4562) covalent geometry : angle 0.57272 ( 6200) hydrogen bonds : bond 0.04207 ( 310) hydrogen bonds : angle 3.47047 ( 924) Misc. bond : bond 0.00061 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.123 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8714 (mm-30) cc_final: 0.8415 (mt-10) REVERT: A 278 GLN cc_start: 0.8297 (mp10) cc_final: 0.7979 (mp10) REVERT: A 290 MET cc_start: 0.7484 (tmm) cc_final: 0.7149 (tpt) REVERT: C 278 GLN cc_start: 0.8299 (mp10) cc_final: 0.7980 (mp10) REVERT: C 290 MET cc_start: 0.7465 (tmm) cc_final: 0.7138 (tpt) outliers start: 5 outliers final: 0 residues processed: 77 average time/residue: 0.7160 time to fit residues: 56.6851 Evaluate side-chains 72 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 104 GLN A 281 HIS C 41 HIS C 104 GLN C 281 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.092469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.069394 restraints weight = 24382.387| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 4.08 r_work: 0.2756 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2739 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2739 r_free = 0.2739 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2739 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4564 Z= 0.139 Angle : 0.574 8.051 6200 Z= 0.305 Chirality : 0.038 0.158 628 Planarity : 0.003 0.028 760 Dihedral : 9.445 83.193 658 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.03 % Allowed : 16.22 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.94 (0.36), residues: 532 helix: 2.80 (0.24), residues: 382 sheet: None (None), residues: 0 loop : -0.39 (0.55), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 265 TYR 0.013 0.001 TYR C 282 PHE 0.008 0.001 PHE C 96 TRP 0.010 0.001 TRP A 211 HIS 0.002 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 4562) covalent geometry : angle 0.57401 ( 6200) hydrogen bonds : bond 0.04198 ( 310) hydrogen bonds : angle 3.39329 ( 924) Misc. bond : bond 0.00063 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.183 Fit side-chains REVERT: A 276 ASN cc_start: 0.8832 (p0) cc_final: 0.8487 (p0) REVERT: A 290 MET cc_start: 0.7576 (tmm) cc_final: 0.7229 (tpt) REVERT: C 276 ASN cc_start: 0.8845 (p0) cc_final: 0.8491 (p0) REVERT: C 290 MET cc_start: 0.7584 (tmm) cc_final: 0.7236 (tpt) outliers start: 9 outliers final: 0 residues processed: 80 average time/residue: 0.7013 time to fit residues: 57.7740 Evaluate side-chains 70 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 49 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 11 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 7.9990 chunk 26 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 104 GLN C 41 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.087254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.063302 restraints weight = 28101.480| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 4.49 r_work: 0.2716 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4564 Z= 0.165 Angle : 0.592 8.381 6200 Z= 0.313 Chirality : 0.039 0.194 628 Planarity : 0.003 0.026 760 Dihedral : 9.568 83.563 658 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 0.68 % Allowed : 17.57 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.93 (0.36), residues: 532 helix: 2.85 (0.24), residues: 380 sheet: -1.84 (1.04), residues: 20 loop : -0.24 (0.61), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 265 TYR 0.012 0.001 TYR C 49 PHE 0.008 0.001 PHE A 96 TRP 0.011 0.001 TRP C 211 HIS 0.002 0.001 HIS A 261 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 4562) covalent geometry : angle 0.59153 ( 6200) hydrogen bonds : bond 0.04362 ( 310) hydrogen bonds : angle 3.36741 ( 924) Misc. bond : bond 0.00079 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.190 Fit side-chains REVERT: A 276 ASN cc_start: 0.9066 (p0) cc_final: 0.8834 (p0) REVERT: A 290 MET cc_start: 0.7636 (tmm) cc_final: 0.7277 (tpt) REVERT: C 276 ASN cc_start: 0.9084 (p0) cc_final: 0.8854 (p0) REVERT: C 290 MET cc_start: 0.7633 (tmm) cc_final: 0.7261 (tpt) outliers start: 3 outliers final: 0 residues processed: 77 average time/residue: 0.7054 time to fit residues: 55.9227 Evaluate side-chains 70 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 0.0020 chunk 16 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 104 GLN C 41 HIS C 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.089022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.065376 restraints weight = 26283.473| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 4.40 r_work: 0.2751 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2762 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2762 r_free = 0.2762 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2762 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4564 Z= 0.128 Angle : 0.563 9.664 6200 Z= 0.303 Chirality : 0.038 0.192 628 Planarity : 0.003 0.027 760 Dihedral : 9.511 88.004 658 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 1.35 % Allowed : 16.89 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.02 (0.37), residues: 532 helix: 2.92 (0.24), residues: 382 sheet: -1.51 (1.12), residues: 20 loop : -0.30 (0.63), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 291 TYR 0.013 0.001 TYR C 49 PHE 0.007 0.001 PHE A 96 TRP 0.009 0.001 TRP C 211 HIS 0.001 0.000 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 4562) covalent geometry : angle 0.56310 ( 6200) hydrogen bonds : bond 0.03991 ( 310) hydrogen bonds : angle 3.28696 ( 924) Misc. bond : bond 0.00050 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 70 time to evaluate : 0.168 Fit side-chains REVERT: A 290 MET cc_start: 0.7602 (tmm) cc_final: 0.7219 (tpt) REVERT: C 290 MET cc_start: 0.7617 (tmm) cc_final: 0.7217 (tpt) outliers start: 6 outliers final: 0 residues processed: 74 average time/residue: 0.6791 time to fit residues: 51.7763 Evaluate side-chains 68 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 16 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS C 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.087414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.062929 restraints weight = 29140.012| |-----------------------------------------------------------------------------| r_work (start): 0.2899 rms_B_bonded: 4.60 r_work: 0.2701 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2720 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4564 Z= 0.151 Angle : 0.584 9.129 6200 Z= 0.311 Chirality : 0.039 0.216 628 Planarity : 0.003 0.026 760 Dihedral : 9.559 85.851 658 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 0.90 % Allowed : 17.34 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.05 (0.37), residues: 532 helix: 2.91 (0.24), residues: 380 sheet: -1.40 (1.15), residues: 20 loop : -0.13 (0.62), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.012 0.001 TYR C 49 PHE 0.008 0.001 PHE A 96 TRP 0.010 0.001 TRP C 211 HIS 0.002 0.001 HIS C 246 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 4562) covalent geometry : angle 0.58374 ( 6200) hydrogen bonds : bond 0.04211 ( 310) hydrogen bonds : angle 3.30904 ( 924) Misc. bond : bond 0.00069 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.150 Fit side-chains REVERT: A 290 MET cc_start: 0.7697 (tmm) cc_final: 0.7249 (tpt) REVERT: C 290 MET cc_start: 0.7693 (tmm) cc_final: 0.7240 (tpt) outliers start: 3 outliers final: 0 residues processed: 69 average time/residue: 0.7483 time to fit residues: 53.0582 Evaluate side-chains 64 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 12 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 0.0060 chunk 36 optimal weight: 2.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS C 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.087315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.062856 restraints weight = 32740.341| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.80 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.3818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4564 Z= 0.152 Angle : 0.593 9.562 6200 Z= 0.319 Chirality : 0.039 0.215 628 Planarity : 0.003 0.025 760 Dihedral : 9.603 87.617 658 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.13 % Allowed : 17.12 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.07 (0.37), residues: 532 helix: 2.91 (0.25), residues: 380 sheet: -1.52 (1.13), residues: 20 loop : -0.05 (0.62), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 265 TYR 0.012 0.001 TYR C 49 PHE 0.010 0.001 PHE C 96 TRP 0.011 0.001 TRP A 211 HIS 0.002 0.001 HIS A 246 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 4562) covalent geometry : angle 0.59333 ( 6200) hydrogen bonds : bond 0.04181 ( 310) hydrogen bonds : angle 3.30452 ( 924) Misc. bond : bond 0.00067 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.157 Fit side-chains REVERT: A 273 HIS cc_start: 0.9092 (t70) cc_final: 0.8862 (t70) REVERT: A 290 MET cc_start: 0.7625 (tmm) cc_final: 0.7227 (tpt) REVERT: C 273 HIS cc_start: 0.9088 (t70) cc_final: 0.8852 (t70) REVERT: C 290 MET cc_start: 0.7615 (tmm) cc_final: 0.7166 (tpt) outliers start: 3 outliers final: 1 residues processed: 72 average time/residue: 0.6873 time to fit residues: 50.9711 Evaluate side-chains 64 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 63 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 11 optimal weight: 0.2980 chunk 31 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 22 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS A 99 HIS C 41 HIS C 99 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.089369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.065473 restraints weight = 25560.517| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.39 r_work: 0.2788 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4564 Z= 0.127 Angle : 0.605 10.214 6200 Z= 0.317 Chirality : 0.038 0.213 628 Planarity : 0.003 0.027 760 Dihedral : 9.413 88.591 658 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.90 % Allowed : 17.34 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.13 (0.37), residues: 532 helix: 2.94 (0.24), residues: 380 sheet: -1.49 (1.16), residues: 20 loop : 0.01 (0.62), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 291 TYR 0.013 0.001 TYR C 49 PHE 0.007 0.001 PHE C 64 TRP 0.008 0.001 TRP A 211 HIS 0.001 0.000 HIS C 99 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4562) covalent geometry : angle 0.60530 ( 6200) hydrogen bonds : bond 0.03917 ( 310) hydrogen bonds : angle 3.26048 ( 924) Misc. bond : bond 0.00047 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 65 time to evaluate : 0.159 Fit side-chains REVERT: A 91 TYR cc_start: 0.8026 (m-80) cc_final: 0.7687 (m-80) REVERT: A 273 HIS cc_start: 0.9157 (t70) cc_final: 0.8926 (t70) REVERT: A 274 THR cc_start: 0.9098 (t) cc_final: 0.8885 (p) REVERT: A 290 MET cc_start: 0.7672 (tmm) cc_final: 0.7245 (tpt) REVERT: C 91 TYR cc_start: 0.8017 (m-80) cc_final: 0.7624 (m-80) REVERT: C 273 HIS cc_start: 0.9155 (t70) cc_final: 0.8925 (t70) REVERT: C 274 THR cc_start: 0.9091 (t) cc_final: 0.8885 (p) REVERT: C 289 LYS cc_start: 0.8916 (mppt) cc_final: 0.8431 (pptt) REVERT: C 290 MET cc_start: 0.7668 (tmm) cc_final: 0.6751 (tpt) outliers start: 2 outliers final: 1 residues processed: 67 average time/residue: 0.7199 time to fit residues: 49.6643 Evaluate side-chains 63 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 62 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS C 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.085855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.061582 restraints weight = 29249.336| |-----------------------------------------------------------------------------| r_work (start): 0.2891 rms_B_bonded: 4.60 r_work: 0.2697 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2695 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2695 r_free = 0.2695 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2695 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 4564 Z= 0.199 Angle : 0.663 9.482 6200 Z= 0.346 Chirality : 0.040 0.212 628 Planarity : 0.003 0.024 760 Dihedral : 9.593 85.190 658 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.13 % Allowed : 17.57 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.03 (0.37), residues: 532 helix: 2.84 (0.25), residues: 380 sheet: -1.65 (1.10), residues: 20 loop : 0.07 (0.61), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 265 TYR 0.010 0.001 TYR A 49 PHE 0.009 0.002 PHE A 199 TRP 0.013 0.001 TRP C 211 HIS 0.003 0.001 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 4562) covalent geometry : angle 0.66253 ( 6200) hydrogen bonds : bond 0.04501 ( 310) hydrogen bonds : angle 3.36097 ( 924) Misc. bond : bond 0.00100 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1064 Ramachandran restraints generated. 532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.120 Fit side-chains REVERT: A 273 HIS cc_start: 0.9190 (t70) cc_final: 0.8963 (t70) REVERT: A 274 THR cc_start: 0.9146 (t) cc_final: 0.8936 (p) REVERT: A 290 MET cc_start: 0.7648 (tmm) cc_final: 0.7208 (tpt) REVERT: C 273 HIS cc_start: 0.9158 (t70) cc_final: 0.8933 (t70) REVERT: C 274 THR cc_start: 0.9148 (t) cc_final: 0.8937 (p) REVERT: C 290 MET cc_start: 0.7683 (tmm) cc_final: 0.7152 (tpt) outliers start: 3 outliers final: 1 residues processed: 69 average time/residue: 0.7125 time to fit residues: 50.5268 Evaluate side-chains 66 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 65 time to evaluate : 0.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 25 optimal weight: 0.0770 chunk 14 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.0010 chunk 8 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 overall best weight: 0.4544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS C 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.088794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.064953 restraints weight = 25733.316| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 4.38 r_work: 0.2765 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2768 r_free = 0.2768 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.3991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4564 Z= 0.127 Angle : 0.612 9.776 6200 Z= 0.322 Chirality : 0.039 0.211 628 Planarity : 0.003 0.027 760 Dihedral : 9.481 87.612 658 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.45 % Allowed : 17.79 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.20 (0.37), residues: 532 helix: 2.88 (0.25), residues: 382 sheet: None (None), residues: 0 loop : 0.08 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG C 265 TYR 0.012 0.001 TYR A 49 PHE 0.007 0.001 PHE C 64 TRP 0.009 0.001 TRP C 211 HIS 0.001 0.000 HIS C 261 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 4562) covalent geometry : angle 0.61227 ( 6200) hydrogen bonds : bond 0.04013 ( 310) hydrogen bonds : angle 3.27617 ( 924) Misc. bond : bond 0.00041 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1849.85 seconds wall clock time: 32 minutes 17.30 seconds (1937.30 seconds total)