Starting phenix.real_space_refine on Wed Jul 23 21:52:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7w_61212/07_2025/9j7w_61212.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7w_61212/07_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_61212/07_2025/9j7w_61212.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7w_61212/07_2025/9j7w_61212.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7w_61212/07_2025/9j7w_61212.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7w_61212/07_2025/9j7w_61212.cif" } resolution = 2.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.91, per 1000 atoms: 1.10 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: 1.31 Conformation dependent library (CDL) restraints added in 998.3 milliseconds 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: 0.41 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: 1.16 Time building geometry restraints manager: 1.51 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: 0.02 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: 2.020 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.360 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.130 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.009 0.001 TRP C 116 HIS 0.006 0.001 HIS C 261 PHE 0.027 0.002 PHE C 85 TYR 0.013 0.001 TYR A 182 ARG 0.003 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.10417 ( 310) hydrogen bonds : angle 5.22509 ( 924) covalent geometry : bond 0.00520 ( 4562) covalent geometry : angle 0.63863 ( 6200) 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 : 0.458 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: 0.8163 (p) outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 1.7594 time to fit residues: 188.3665 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 : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 = 0.3411 r_free = 0.3411 target = 0.090106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.066402 restraints weight = 25838.212| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 4.33 r_work: 0.2766 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.2766 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2749 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2749 r_free = 0.2749 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2749 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4564 Z= 0.168 Angle : 0.644 11.684 6200 Z= 0.337 Chirality : 0.039 0.173 628 Planarity : 0.003 0.029 760 Dihedral : 9.794 79.583 658 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.25 % Allowed : 11.26 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.36), residues: 532 helix: 2.66 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -0.73 (0.53), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.002 0.001 HIS C 261 PHE 0.009 0.001 PHE C 66 TYR 0.022 0.001 TYR C 49 ARG 0.001 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 310) hydrogen bonds : angle 3.66571 ( 924) covalent geometry : bond 0.00385 ( 4562) covalent geometry : angle 0.64368 ( 6200) Misc. bond : bond 0.00125 ( 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 : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 290 MET cc_start: 0.7348 (tmm) cc_final: 0.7116 (tpt) REVERT: C 290 MET cc_start: 0.7336 (tmm) cc_final: 0.7106 (tpt) outliers start: 10 outliers final: 1 residues processed: 92 average time/residue: 1.4080 time to fit residues: 133.8310 Evaluate side-chains 74 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 73 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 36 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 22 optimal weight: 0.6980 chunk 35 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 8 optimal weight: 0.7980 chunk 5 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 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 = 0.3452 r_free = 0.3452 target = 0.092822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.069719 restraints weight = 25189.965| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 4.13 r_work: 0.2743 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2742 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2742 r_free = 0.2742 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2742 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3274 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= 0.140 Angle : 0.573 7.450 6200 Z= 0.304 Chirality : 0.038 0.161 628 Planarity : 0.003 0.028 760 Dihedral : 9.503 82.508 658 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.58 % Allowed : 15.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.36), residues: 532 helix: 2.85 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -0.45 (0.55), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 211 HIS 0.002 0.001 HIS C 261 PHE 0.008 0.001 PHE A 85 TYR 0.016 0.001 TYR C 49 ARG 0.001 0.000 ARG A 291 Details of bonding type rmsd hydrogen bonds : bond 0.04233 ( 310) hydrogen bonds : angle 3.45838 ( 924) covalent geometry : bond 0.00315 ( 4562) covalent geometry : angle 0.57265 ( 6200) Misc. bond : bond 0.00067 ( 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 85 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.517 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8740 (mm-30) cc_final: 0.8450 (mt-10) REVERT: A 278 GLN cc_start: 0.8394 (mp10) cc_final: 0.8059 (mp10) REVERT: A 290 MET cc_start: 0.7516 (tmm) cc_final: 0.7151 (tpt) REVERT: C 94 GLU cc_start: 0.8710 (mm-30) cc_final: 0.8463 (mt-10) REVERT: C 276 ASN cc_start: 0.8935 (p0) cc_final: 0.8663 (p0) REVERT: C 290 MET cc_start: 0.7516 (tmm) cc_final: 0.7152 (tpt) outliers start: 7 outliers final: 0 residues processed: 83 average time/residue: 1.8983 time to fit residues: 163.2838 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 : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 33 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3339 r_free = 0.3339 target = 0.085582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.062057 restraints weight = 19634.633| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.92 r_work: 0.2706 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.3537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4564 Z= 0.203 Angle : 0.632 8.173 6200 Z= 0.333 Chirality : 0.041 0.184 628 Planarity : 0.003 0.027 760 Dihedral : 9.767 80.976 658 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.35 % Allowed : 17.57 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.83 (0.36), residues: 532 helix: 2.72 (0.24), residues: 380 sheet: None (None), residues: 0 loop : -0.39 (0.56), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.003 0.001 HIS A 261 PHE 0.009 0.002 PHE C 175 TYR 0.013 0.001 TYR C 49 ARG 0.002 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 310) hydrogen bonds : angle 3.47842 ( 924) covalent geometry : bond 0.00478 ( 4562) covalent geometry : angle 0.63164 ( 6200) Misc. bond : bond 0.00103 ( 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 78 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 72 time to evaluate : 0.623 Fit side-chains REVERT: A 94 GLU cc_start: 0.8694 (mm-30) cc_final: 0.8450 (mt-10) REVERT: A 276 ASN cc_start: 0.8891 (p0) cc_final: 0.8629 (p0) REVERT: A 290 MET cc_start: 0.7635 (tmm) cc_final: 0.7261 (tpt) REVERT: C 94 GLU cc_start: 0.8670 (mm-30) cc_final: 0.8403 (mt-10) REVERT: C 276 ASN cc_start: 0.9017 (p0) cc_final: 0.8806 (p0) REVERT: C 290 MET cc_start: 0.7619 (tmm) cc_final: 0.7252 (tpt) outliers start: 6 outliers final: 0 residues processed: 76 average time/residue: 2.5715 time to fit residues: 201.7489 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 : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 26 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 9 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 25 optimal weight: 0.4980 chunk 8 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3356 r_free = 0.3356 target = 0.086523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.062837 restraints weight = 25664.156| |-----------------------------------------------------------------------------| r_work (start): 0.2894 rms_B_bonded: 4.36 r_work: 0.2708 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.3610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4564 Z= 0.164 Angle : 0.593 8.280 6200 Z= 0.315 Chirality : 0.039 0.188 628 Planarity : 0.003 0.026 760 Dihedral : 9.773 86.897 658 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.58 % Allowed : 15.99 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.90 (0.36), residues: 532 helix: 2.72 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -0.25 (0.56), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 211 HIS 0.002 0.001 HIS C 261 PHE 0.007 0.001 PHE C 96 TYR 0.013 0.001 TYR A 49 ARG 0.002 0.000 ARG C 265 Details of bonding type rmsd hydrogen bonds : bond 0.04403 ( 310) hydrogen bonds : angle 3.38083 ( 924) covalent geometry : bond 0.00381 ( 4562) covalent geometry : angle 0.59342 ( 6200) Misc. bond : bond 0.00077 ( 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 79 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 1.050 Fit side-chains REVERT: A 276 ASN cc_start: 0.9077 (p0) cc_final: 0.8870 (p0) REVERT: A 290 MET cc_start: 0.7629 (tmm) cc_final: 0.7227 (tpt) REVERT: C 94 GLU cc_start: 0.8719 (mm-30) cc_final: 0.8514 (mt-10) REVERT: C 276 ASN cc_start: 0.9086 (p0) cc_final: 0.8878 (p0) REVERT: C 290 MET cc_start: 0.7602 (tmm) cc_final: 0.7222 (tpt) outliers start: 7 outliers final: 0 residues processed: 77 average time/residue: 1.8621 time to fit residues: 148.3069 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 : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 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 C 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.088130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.064433 restraints weight = 25185.378| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 4.32 r_work: 0.2728 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2737 r_free = 0.2737 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.3733 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= 0.135 Angle : 0.582 9.466 6200 Z= 0.311 Chirality : 0.038 0.188 628 Planarity : 0.003 0.026 760 Dihedral : 9.708 89.097 658 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.90 % Allowed : 17.12 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.36), residues: 532 helix: 2.80 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -0.23 (0.56), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 211 HIS 0.002 0.000 HIS A 246 PHE 0.007 0.001 PHE C 64 TYR 0.013 0.001 TYR C 49 ARG 0.001 0.000 ARG C 291 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 310) hydrogen bonds : angle 3.31317 ( 924) covalent geometry : bond 0.00305 ( 4562) covalent geometry : angle 0.58192 ( 6200) Misc. bond : bond 0.00059 ( 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 71 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.458 Fit side-chains REVERT: A 290 MET cc_start: 0.7677 (tmm) cc_final: 0.7210 (tpt) REVERT: C 290 MET cc_start: 0.7642 (tmm) cc_final: 0.7188 (tpt) outliers start: 2 outliers final: 0 residues processed: 71 average time/residue: 1.3881 time to fit residues: 102.1617 Evaluate side-chains 67 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 7 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 15 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 45 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 = 0.3365 r_free = 0.3365 target = 0.086904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.062835 restraints weight = 24390.776| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.31 r_work: 0.2729 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2724 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2724 r_free = 0.2724 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2724 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.3810 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= 0.150 Angle : 0.584 9.114 6200 Z= 0.312 Chirality : 0.038 0.216 628 Planarity : 0.003 0.026 760 Dihedral : 9.731 89.944 658 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 1.13 % Allowed : 16.67 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.37), residues: 532 helix: 2.83 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -0.19 (0.56), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.002 0.001 HIS C 261 PHE 0.008 0.001 PHE A 96 TYR 0.013 0.001 TYR A 49 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04175 ( 310) hydrogen bonds : angle 3.29287 ( 924) covalent geometry : bond 0.00346 ( 4562) covalent geometry : angle 0.58421 ( 6200) Misc. bond : bond 0.00068 ( 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 : 0.571 Fit side-chains REVERT: A 94 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8364 (mt-10) REVERT: A 273 HIS cc_start: 0.9177 (t70) cc_final: 0.8943 (t70) REVERT: A 274 THR cc_start: 0.9136 (t) cc_final: 0.8919 (p) REVERT: A 290 MET cc_start: 0.7676 (tmm) cc_final: 0.7196 (tpt) REVERT: C 273 HIS cc_start: 0.9154 (t70) cc_final: 0.8923 (t70) REVERT: C 274 THR cc_start: 0.9116 (t) cc_final: 0.8908 (p) REVERT: C 290 MET cc_start: 0.7672 (tmm) cc_final: 0.7193 (tpt) outliers start: 3 outliers final: 2 residues processed: 70 average time/residue: 1.6108 time to fit residues: 116.6151 Evaluate side-chains 68 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 66 time to evaluate : 0.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain C residue 52 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 27 optimal weight: 9.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3357 r_free = 0.3357 target = 0.086440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.062086 restraints weight = 31113.487| |-----------------------------------------------------------------------------| r_work (start): 0.2906 rms_B_bonded: 4.67 r_work: 0.2708 rms_B_bonded: 4.92 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4564 Z= 0.155 Angle : 0.591 9.460 6200 Z= 0.315 Chirality : 0.038 0.216 628 Planarity : 0.003 0.026 760 Dihedral : 9.761 89.974 658 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.13 % Allowed : 16.67 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.37), residues: 532 helix: 2.81 (0.25), residues: 382 sheet: None (None), residues: 0 loop : -0.08 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.002 0.001 HIS C 246 PHE 0.008 0.001 PHE A 96 TYR 0.012 0.001 TYR A 49 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 310) hydrogen bonds : angle 3.28180 ( 924) covalent geometry : bond 0.00360 ( 4562) covalent geometry : angle 0.59133 ( 6200) Misc. bond : bond 0.00071 ( 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 70 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.510 Fit side-chains REVERT: A 94 GLU cc_start: 0.8617 (mt-10) cc_final: 0.8283 (mt-10) REVERT: A 273 HIS cc_start: 0.9187 (t70) cc_final: 0.8967 (t70) REVERT: A 274 THR cc_start: 0.9155 (t) cc_final: 0.8926 (p) REVERT: A 290 MET cc_start: 0.7651 (tmm) cc_final: 0.7138 (tpt) REVERT: C 273 HIS cc_start: 0.9179 (t70) cc_final: 0.8962 (t70) REVERT: C 274 THR cc_start: 0.9155 (t) cc_final: 0.8936 (p) REVERT: C 290 MET cc_start: 0.7650 (tmm) cc_final: 0.7135 (tpt) outliers start: 3 outliers final: 3 residues processed: 69 average time/residue: 1.4563 time to fit residues: 103.7709 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 : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 154 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 19 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3362 r_free = 0.3362 target = 0.086744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.062583 restraints weight = 25192.546| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 4.36 r_work: 0.2726 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.2726 ------------------------------------------------------------------------------- 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 = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2720 r_free = 0.2720 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2720 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3902 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= 0.150 Angle : 0.590 9.720 6200 Z= 0.314 Chirality : 0.038 0.215 628 Planarity : 0.003 0.026 760 Dihedral : 9.739 89.705 658 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.13 % Allowed : 16.67 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.37), residues: 532 helix: 2.82 (0.25), residues: 382 sheet: None (None), residues: 0 loop : 0.00 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.002 0.000 HIS C 246 PHE 0.008 0.001 PHE C 96 TYR 0.012 0.001 TYR A 49 ARG 0.001 0.000 ARG A 265 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 310) hydrogen bonds : angle 3.27492 ( 924) covalent geometry : bond 0.00348 ( 4562) covalent geometry : angle 0.58951 ( 6200) Misc. bond : bond 0.00070 ( 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 69 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 66 time to evaluate : 0.454 Fit side-chains REVERT: A 273 HIS cc_start: 0.9192 (t70) cc_final: 0.8969 (t70) REVERT: A 274 THR cc_start: 0.9173 (t) cc_final: 0.8934 (p) REVERT: A 289 LYS cc_start: 0.8929 (mppt) cc_final: 0.8439 (pptt) REVERT: A 290 MET cc_start: 0.7610 (tmm) cc_final: 0.6707 (tpt) REVERT: C 94 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8307 (mt-10) REVERT: C 200 THR cc_start: 0.8821 (t) cc_final: 0.8561 (p) REVERT: C 273 HIS cc_start: 0.9201 (t70) cc_final: 0.8979 (t70) REVERT: C 274 THR cc_start: 0.9167 (t) cc_final: 0.8936 (p) REVERT: C 289 LYS cc_start: 0.8927 (mppt) cc_final: 0.8438 (pptt) REVERT: C 290 MET cc_start: 0.7611 (tmm) cc_final: 0.6706 (tpt) outliers start: 3 outliers final: 3 residues processed: 68 average time/residue: 1.4194 time to fit residues: 99.8450 Evaluate side-chains 66 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 63 time to evaluate : 0.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 154 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 47 optimal weight: 3.9990 chunk 20 optimal weight: 0.2980 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 24 optimal weight: 0.4980 chunk 40 optimal weight: 0.6980 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 C 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.088409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.064414 restraints weight = 26649.944| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 4.47 r_work: 0.2764 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2753 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2753 r_free = 0.2753 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2753 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3975 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= 0.123 Angle : 0.568 9.353 6200 Z= 0.305 Chirality : 0.038 0.203 628 Planarity : 0.003 0.027 760 Dihedral : 9.416 84.830 658 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.90 % Allowed : 16.89 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.37), residues: 532 helix: 2.89 (0.25), residues: 382 sheet: None (None), residues: 0 loop : 0.00 (0.58), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 211 HIS 0.001 0.000 HIS A 246 PHE 0.011 0.001 PHE A 199 TYR 0.013 0.001 TYR A 49 ARG 0.000 0.000 ARG C 265 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 310) hydrogen bonds : angle 3.22057 ( 924) covalent geometry : bond 0.00271 ( 4562) covalent geometry : angle 0.56802 ( 6200) Misc. bond : bond 0.00048 ( 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 70 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 68 time to evaluate : 0.466 Fit side-chains REVERT: A 91 TYR cc_start: 0.8023 (m-80) cc_final: 0.7636 (m-80) REVERT: A 200 THR cc_start: 0.8792 (t) cc_final: 0.8553 (p) REVERT: A 273 HIS cc_start: 0.9192 (t70) cc_final: 0.8983 (t70) REVERT: A 274 THR cc_start: 0.9178 (t) cc_final: 0.8940 (p) REVERT: A 289 LYS cc_start: 0.8939 (mppt) cc_final: 0.8454 (pptt) REVERT: A 290 MET cc_start: 0.7606 (tmm) cc_final: 0.6753 (tpt) REVERT: C 91 TYR cc_start: 0.8018 (m-80) cc_final: 0.7689 (m-80) REVERT: C 94 GLU cc_start: 0.8551 (mt-10) cc_final: 0.8255 (mt-10) REVERT: C 154 ASP cc_start: 0.9371 (t70) cc_final: 0.9090 (t0) REVERT: C 200 THR cc_start: 0.8801 (t) cc_final: 0.8521 (p) REVERT: C 273 HIS cc_start: 0.9203 (t70) cc_final: 0.8993 (t70) REVERT: C 274 THR cc_start: 0.9176 (t) cc_final: 0.8943 (p) REVERT: C 289 LYS cc_start: 0.8927 (mppt) cc_final: 0.8450 (pptt) REVERT: C 290 MET cc_start: 0.7605 (tmm) cc_final: 0.6751 (tpt) outliers start: 2 outliers final: 2 residues processed: 70 average time/residue: 1.3088 time to fit residues: 94.9532 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 : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain C residue 52 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 42 optimal weight: 0.8980 chunk 11 optimal weight: 0.0270 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.2980 chunk 24 optimal weight: 0.1980 overall best weight: 0.3838 ------------------------------------------------------------------------------- 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 = 0.3407 r_free = 0.3407 target = 0.089456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.066052 restraints weight = 18853.146| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.98 r_work: 0.2804 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2809 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2809 r_free = 0.2809 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2809 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.4040 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= 0.118 Angle : 0.554 9.174 6200 Z= 0.297 Chirality : 0.037 0.212 628 Planarity : 0.003 0.027 760 Dihedral : 9.206 83.302 658 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.90 % Allowed : 17.12 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.26 (0.37), residues: 532 helix: 2.93 (0.25), residues: 382 sheet: None (None), residues: 0 loop : 0.08 (0.57), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 211 HIS 0.001 0.000 HIS A 246 PHE 0.007 0.001 PHE C 64 TYR 0.014 0.001 TYR A 49 ARG 0.000 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03731 ( 310) hydrogen bonds : angle 3.17532 ( 924) covalent geometry : bond 0.00258 ( 4562) covalent geometry : angle 0.55443 ( 6200) Misc. bond : bond 0.00043 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4397.25 seconds wall clock time: 79 minutes 24.91 seconds (4764.91 seconds total)