Starting phenix.real_space_refine on Wed Sep 17 04:16:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bim_44593/09_2025/9bim_44593.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bim_44593/09_2025/9bim_44593.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bim_44593/09_2025/9bim_44593.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bim_44593/09_2025/9bim_44593.map" model { file = "/net/cci-nas-00/data/ceres_data/9bim_44593/09_2025/9bim_44593.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bim_44593/09_2025/9bim_44593.cif" } resolution = 3.67 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= 0.207 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2665 2.51 5 N 605 2.21 5 O 702 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: 3992 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3962 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 3962 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 493} Chain breaks: 1 Chain: "A" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'HC6': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.29, per 1000 atoms: 0.32 Number of scatterers: 3992 At special positions: 0 Unit cell: (58.8, 83.16, 84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 702 8.00 N 605 7.00 C 2665 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 157.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 73.8% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'A' and resid 4 through 29 removed outlier: 3.737A pdb=" N LEU A 8 " --> pdb=" O HIS A 4 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N ALA A 10 " --> pdb=" O GLU A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 44 removed outlier: 4.092A pdb=" N ILE A 43 " --> pdb=" O SER A 39 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N VAL A 44 " --> pdb=" O GLU A 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 39 through 44' Processing helix chain 'A' and resid 51 through 63 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 86 through 102 Processing helix chain 'A' and resid 102 through 109 removed outlier: 3.611A pdb=" N MET A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LYS A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 157 removed outlier: 3.501A pdb=" N ILE A 121 " --> pdb=" O PRO A 117 " (cutoff:3.500A) removed outlier: 7.872A pdb=" N LYS A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) removed outlier: 9.230A pdb=" N ARG A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N MET A 126 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Proline residue: A 133 - end of helix Processing helix chain 'A' and resid 160 through 179 removed outlier: 3.671A pdb=" N SER A 164 " --> pdb=" O ASP A 160 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL A 165 " --> pdb=" O MET A 161 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE A 166 " --> pdb=" O HIS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 208 removed outlier: 3.969A pdb=" N PHE A 193 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER A 202 " --> pdb=" O GLY A 198 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N VAL A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix Processing helix chain 'A' and resid 214 through 221 removed outlier: 3.714A pdb=" N ALA A 219 " --> pdb=" O ILE A 215 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL A 220 " --> pdb=" O GLY A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 250 Processing helix chain 'A' and resid 254 through 263 removed outlier: 4.321A pdb=" N ARG A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 263 " --> pdb=" O GLN A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 298 removed outlier: 3.529A pdb=" N GLN A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) Proline residue: A 287 - end of helix Processing helix chain 'A' and resid 319 through 327 Processing helix chain 'A' and resid 329 through 360 removed outlier: 3.604A pdb=" N PHE A 359 " --> pdb=" O ALA A 355 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 360 " --> pdb=" O SER A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 399 Processing helix chain 'A' and resid 401 through 426 removed outlier: 3.631A pdb=" N LEU A 405 " --> pdb=" O THR A 401 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE A 418 " --> pdb=" O TYR A 414 " (cutoff:3.500A) Proline residue: A 419 - end of helix removed outlier: 3.757A pdb=" N LEU A 425 " --> pdb=" O LEU A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 431 through 450 removed outlier: 3.544A pdb=" N ALA A 435 " --> pdb=" O ASN A 431 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467 262 hydrogen bonds defined for protein. 777 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: 0.60 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1153 1.34 - 1.46: 753 1.46 - 1.57: 2165 1.57 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 4106 Sorted by residual: bond pdb=" CAS HC6 A 701 " pdb=" OBD HC6 A 701 " ideal model delta sigma weight residual 1.389 1.430 -0.041 2.00e-02 2.50e+03 4.19e+00 bond pdb=" CAB HC6 A 701 " pdb=" NAA HC6 A 701 " ideal model delta sigma weight residual 1.500 1.459 0.041 2.00e-02 2.50e+03 4.16e+00 bond pdb=" CAC HC6 A 701 " pdb=" NAA HC6 A 701 " ideal model delta sigma weight residual 1.502 1.467 0.035 2.00e-02 2.50e+03 3.06e+00 bond pdb=" CAD HC6 A 701 " pdb=" OBC HC6 A 701 " ideal model delta sigma weight residual 1.389 1.423 -0.034 2.00e-02 2.50e+03 2.98e+00 bond pdb=" CAX HC6 A 701 " pdb=" NAW HC6 A 701 " ideal model delta sigma weight residual 1.502 1.468 0.034 2.00e-02 2.50e+03 2.81e+00 ... (remaining 4101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 5478 2.04 - 4.07: 104 4.07 - 6.11: 22 6.11 - 8.14: 9 8.14 - 10.18: 1 Bond angle restraints: 5614 Sorted by residual: angle pdb=" CA TYR A 175 " pdb=" CB TYR A 175 " pdb=" CG TYR A 175 " ideal model delta sigma weight residual 113.90 119.67 -5.77 1.80e+00 3.09e-01 1.03e+01 angle pdb=" N GLY A 179 " pdb=" CA GLY A 179 " pdb=" C GLY A 179 " ideal model delta sigma weight residual 113.18 120.19 -7.01 2.37e+00 1.78e-01 8.75e+00 angle pdb=" CA LEU A 273 " pdb=" CB LEU A 273 " pdb=" CG LEU A 273 " ideal model delta sigma weight residual 116.30 126.48 -10.18 3.50e+00 8.16e-02 8.46e+00 angle pdb=" C VAL A 178 " pdb=" N GLY A 179 " pdb=" CA GLY A 179 " ideal model delta sigma weight residual 121.41 115.93 5.48 1.96e+00 2.60e-01 7.81e+00 angle pdb=" CG ARG A 38 " pdb=" CD ARG A 38 " pdb=" NE ARG A 38 " ideal model delta sigma weight residual 112.00 118.13 -6.13 2.20e+00 2.07e-01 7.76e+00 ... (remaining 5609 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.67: 2101 14.67 - 29.33: 179 29.33 - 44.00: 61 44.00 - 58.66: 4 58.66 - 73.33: 7 Dihedral angle restraints: 2352 sinusoidal: 869 harmonic: 1483 Sorted by residual: dihedral pdb=" CA LYS A 109 " pdb=" C LYS A 109 " pdb=" N GLY A 110 " pdb=" CA GLY A 110 " ideal model delta harmonic sigma weight residual -180.00 -161.03 -18.97 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA MET A 114 " pdb=" C MET A 114 " pdb=" N LEU A 115 " pdb=" CA LEU A 115 " ideal model delta harmonic sigma weight residual 180.00 -162.11 -17.89 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA GLY A 7 " pdb=" C GLY A 7 " pdb=" N LEU A 8 " pdb=" CA LEU A 8 " ideal model delta harmonic sigma weight residual 180.00 163.07 16.93 0 5.00e+00 4.00e-02 1.15e+01 ... (remaining 2349 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 476 0.045 - 0.090: 132 0.090 - 0.136: 33 0.136 - 0.181: 5 0.181 - 0.226: 1 Chirality restraints: 647 Sorted by residual: chirality pdb=" CB VAL A 44 " pdb=" CA VAL A 44 " pdb=" CG1 VAL A 44 " pdb=" CG2 VAL A 44 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB VAL A 184 " pdb=" CA VAL A 184 " pdb=" CG1 VAL A 184 " pdb=" CG2 VAL A 184 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.54e-01 chirality pdb=" CB ILE A 157 " pdb=" CA ILE A 157 " pdb=" CG1 ILE A 157 " pdb=" CG2 ILE A 157 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 644 not shown) Planarity restraints: 680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 175 " 0.012 2.00e-02 2.50e+03 1.05e-02 2.19e+00 pdb=" CG TYR A 175 " -0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 175 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR A 175 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 175 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 175 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 175 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 175 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 418 " 0.024 5.00e-02 4.00e+02 3.56e-02 2.02e+00 pdb=" N PRO A 419 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 116 " 0.021 5.00e-02 4.00e+02 3.20e-02 1.64e+00 pdb=" N PRO A 117 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO A 117 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 117 " 0.018 5.00e-02 4.00e+02 ... (remaining 677 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 944 2.79 - 3.32: 3830 3.32 - 3.84: 6747 3.84 - 4.37: 7356 4.37 - 4.90: 13195 Nonbonded interactions: 32072 Sorted by model distance: nonbonded pdb=" O ILE A 294 " pdb=" OG1 THR A 298 " model vdw 2.259 3.040 nonbonded pdb=" O VAL A 380 " pdb=" OG1 THR A 384 " model vdw 2.320 3.040 nonbonded pdb=" OD2 ASP A 309 " pdb=" NZ LYS A 311 " model vdw 2.361 3.120 nonbonded pdb=" O ALA A 60 " pdb=" OG SER A 346 " model vdw 2.450 3.040 nonbonded pdb=" OH TYR A 305 " pdb=" OE1 GLU A 315 " model vdw 2.458 3.040 ... (remaining 32067 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.000 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.150 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 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 : 0.004 0.044 4106 Z= 0.186 Angle : 0.745 10.179 5614 Z= 0.365 Chirality : 0.045 0.226 647 Planarity : 0.005 0.040 680 Dihedral : 13.024 73.329 1414 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.00 (0.35), residues: 512 helix: 0.49 (0.26), residues: 359 sheet: None (None), residues: 0 loop : -0.97 (0.46), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 38 TYR 0.026 0.002 TYR A 175 PHE 0.021 0.002 PHE A 258 TRP 0.010 0.001 TRP A 62 HIS 0.002 0.001 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00400 ( 4106) covalent geometry : angle 0.74544 ( 5614) hydrogen bonds : bond 0.12241 ( 262) hydrogen bonds : angle 5.39522 ( 777) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.133 Fit side-chains REVERT: A 106 MET cc_start: 0.7221 (mmt) cc_final: 0.6655 (mmt) REVERT: A 269 TYR cc_start: 0.8135 (m-10) cc_final: 0.7855 (m-10) REVERT: A 484 MET cc_start: 0.8321 (tmm) cc_final: 0.7986 (ttt) outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.0858 time to fit residues: 2.7006 Evaluate side-chains 22 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 24 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.141588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.111395 restraints weight = 4190.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.114107 restraints weight = 2792.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.115741 restraints weight = 2154.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117180 restraints weight = 1835.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.117673 restraints weight = 1649.487| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.0815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4106 Z= 0.155 Angle : 0.590 7.968 5614 Z= 0.295 Chirality : 0.040 0.140 647 Planarity : 0.004 0.026 680 Dihedral : 8.205 58.621 591 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.72 % Allowed : 6.28 % Favored : 93.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.72 (0.37), residues: 512 helix: 1.01 (0.27), residues: 364 sheet: None (None), residues: 0 loop : -0.70 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 38 TYR 0.024 0.001 TYR A 67 PHE 0.011 0.001 PHE A 244 TRP 0.006 0.001 TRP A 254 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 4106) covalent geometry : angle 0.58993 ( 5614) hydrogen bonds : bond 0.04367 ( 262) hydrogen bonds : angle 4.34677 ( 777) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 22 time to evaluate : 0.137 Fit side-chains REVERT: A 106 MET cc_start: 0.7403 (mmt) cc_final: 0.6761 (mmt) REVERT: A 269 TYR cc_start: 0.8253 (m-10) cc_final: 0.7986 (m-80) REVERT: A 484 MET cc_start: 0.8600 (tmm) cc_final: 0.7843 (ttt) outliers start: 3 outliers final: 2 residues processed: 23 average time/residue: 0.0883 time to fit residues: 2.6180 Evaluate side-chains 23 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 0.0370 chunk 11 optimal weight: 0.8980 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 23 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.143069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.112375 restraints weight = 4174.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.115369 restraints weight = 2713.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117439 restraints weight = 2050.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.118777 restraints weight = 1737.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.119446 restraints weight = 1554.123| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4106 Z= 0.123 Angle : 0.534 6.719 5614 Z= 0.266 Chirality : 0.039 0.135 647 Planarity : 0.003 0.024 680 Dihedral : 6.590 43.469 591 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.97 % Allowed : 8.94 % Favored : 90.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.21 (0.37), residues: 512 helix: 1.37 (0.28), residues: 365 sheet: None (None), residues: 0 loop : -0.54 (0.49), residues: 147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 38 TYR 0.022 0.001 TYR A 175 PHE 0.008 0.001 PHE A 244 TRP 0.007 0.001 TRP A 24 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 4106) covalent geometry : angle 0.53356 ( 5614) hydrogen bonds : bond 0.03970 ( 262) hydrogen bonds : angle 4.04442 ( 777) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 26 time to evaluate : 0.147 Fit side-chains REVERT: A 109 LYS cc_start: 0.7360 (pttm) cc_final: 0.7002 (ptpt) REVERT: A 269 TYR cc_start: 0.8218 (m-10) cc_final: 0.7851 (m-80) outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.0939 time to fit residues: 3.3141 Evaluate side-chains 25 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 23 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 358 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 17 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 9 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 46 optimal weight: 9.9990 chunk 25 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.110297 restraints weight = 4179.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.113256 restraints weight = 2719.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.115160 restraints weight = 2085.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.116392 restraints weight = 1754.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.117485 restraints weight = 1573.463| |-----------------------------------------------------------------------------| r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4106 Z= 0.133 Angle : 0.541 8.525 5614 Z= 0.268 Chirality : 0.039 0.143 647 Planarity : 0.004 0.024 680 Dihedral : 6.406 42.714 591 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.97 % Allowed : 9.66 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.46 (0.38), residues: 512 helix: 1.49 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -0.35 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 38 TYR 0.022 0.001 TYR A 175 PHE 0.008 0.001 PHE A 479 TRP 0.006 0.001 TRP A 24 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 4106) covalent geometry : angle 0.54100 ( 5614) hydrogen bonds : bond 0.03944 ( 262) hydrogen bonds : angle 4.03617 ( 777) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.149 Fit side-chains REVERT: A 109 LYS cc_start: 0.7377 (pttm) cc_final: 0.7117 (ptpt) REVERT: A 269 TYR cc_start: 0.8264 (m-10) cc_final: 0.7837 (m-80) REVERT: A 484 MET cc_start: 0.8657 (tmm) cc_final: 0.7825 (ttt) outliers start: 4 outliers final: 1 residues processed: 25 average time/residue: 0.0969 time to fit residues: 3.0565 Evaluate side-chains 24 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 23 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 283 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 11 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 4 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.140335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.109387 restraints weight = 4180.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.112363 restraints weight = 2724.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.114188 restraints weight = 2084.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.115625 restraints weight = 1769.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116251 restraints weight = 1585.834| |-----------------------------------------------------------------------------| r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4106 Z= 0.131 Angle : 0.541 8.241 5614 Z= 0.265 Chirality : 0.039 0.141 647 Planarity : 0.003 0.027 680 Dihedral : 6.137 40.706 591 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.17 % Allowed : 8.94 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.58 (0.38), residues: 512 helix: 1.58 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -0.34 (0.51), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 38 TYR 0.022 0.001 TYR A 175 PHE 0.007 0.001 PHE A 244 TRP 0.006 0.001 TRP A 24 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 4106) covalent geometry : angle 0.54133 ( 5614) hydrogen bonds : bond 0.03912 ( 262) hydrogen bonds : angle 3.99277 ( 777) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 24 time to evaluate : 0.085 Fit side-chains REVERT: A 109 LYS cc_start: 0.7373 (pttm) cc_final: 0.7130 (ptpt) REVERT: A 139 MET cc_start: 0.6926 (mmm) cc_final: 0.5456 (ttp) REVERT: A 187 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8099 (m) REVERT: A 484 MET cc_start: 0.8616 (tmm) cc_final: 0.7754 (ttt) outliers start: 9 outliers final: 4 residues processed: 32 average time/residue: 0.0764 time to fit residues: 3.1399 Evaluate side-chains 28 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 422 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 29 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 33 optimal weight: 0.5980 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 11 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.140315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.109365 restraints weight = 4233.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.112416 restraints weight = 2742.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.114582 restraints weight = 2082.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115938 restraints weight = 1730.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116179 restraints weight = 1558.094| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4106 Z= 0.128 Angle : 0.522 7.972 5614 Z= 0.259 Chirality : 0.039 0.140 647 Planarity : 0.003 0.025 680 Dihedral : 5.895 38.776 591 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.66 % Allowed : 8.21 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.58 (0.38), residues: 512 helix: 1.60 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.34 (0.50), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 38 TYR 0.022 0.001 TYR A 175 PHE 0.007 0.001 PHE A 479 TRP 0.006 0.001 TRP A 240 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 4106) covalent geometry : angle 0.52183 ( 5614) hydrogen bonds : bond 0.03857 ( 262) hydrogen bonds : angle 3.96531 ( 777) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 23 time to evaluate : 0.141 Fit side-chains REVERT: A 187 THR cc_start: 0.8272 (OUTLIER) cc_final: 0.8058 (m) outliers start: 11 outliers final: 6 residues processed: 30 average time/residue: 0.0849 time to fit residues: 3.2366 Evaluate side-chains 30 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 23 time to evaluate : 0.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 LEU Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 422 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.1980 chunk 44 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 32 optimal weight: 0.4980 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.141322 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.110305 restraints weight = 4164.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.113345 restraints weight = 2711.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115478 restraints weight = 2056.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.116566 restraints weight = 1731.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117599 restraints weight = 1561.182| |-----------------------------------------------------------------------------| r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4106 Z= 0.118 Angle : 0.520 7.557 5614 Z= 0.256 Chirality : 0.038 0.139 647 Planarity : 0.004 0.028 680 Dihedral : 5.607 35.886 591 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.93 % Allowed : 8.94 % Favored : 89.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.83 (0.38), residues: 512 helix: 1.78 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.16 (0.50), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 369 TYR 0.022 0.001 TYR A 175 PHE 0.016 0.001 PHE A 258 TRP 0.006 0.001 TRP A 240 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 4106) covalent geometry : angle 0.52024 ( 5614) hydrogen bonds : bond 0.03748 ( 262) hydrogen bonds : angle 3.91943 ( 777) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.139 Fit side-chains REVERT: A 139 MET cc_start: 0.6980 (mmm) cc_final: 0.5346 (ttp) REVERT: A 187 THR cc_start: 0.8214 (OUTLIER) cc_final: 0.7989 (m) REVERT: A 484 MET cc_start: 0.8622 (tmm) cc_final: 0.7936 (ttt) outliers start: 8 outliers final: 5 residues processed: 29 average time/residue: 0.0901 time to fit residues: 3.2937 Evaluate side-chains 31 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 25 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 283 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Chi-restraints excluded: chain A residue 422 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 39 optimal weight: 0.1980 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.0010 chunk 15 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 chunk 41 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 42 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 0.1980 overall best weight: 0.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.146399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.116096 restraints weight = 4103.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.119145 restraints weight = 2635.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.121462 restraints weight = 1974.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.122634 restraints weight = 1648.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.123582 restraints weight = 1475.906| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4106 Z= 0.099 Angle : 0.484 6.400 5614 Z= 0.241 Chirality : 0.037 0.136 647 Planarity : 0.003 0.027 680 Dihedral : 4.789 26.791 591 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.45 % Allowed : 9.66 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 2.10 (0.38), residues: 512 helix: 1.98 (0.28), residues: 367 sheet: None (None), residues: 0 loop : -0.05 (0.51), residues: 145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 369 TYR 0.024 0.001 TYR A 175 PHE 0.010 0.001 PHE A 258 TRP 0.007 0.001 TRP A 240 HIS 0.001 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 4106) covalent geometry : angle 0.48442 ( 5614) hydrogen bonds : bond 0.03432 ( 262) hydrogen bonds : angle 3.71401 ( 777) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.123 Fit side-chains REVERT: A 139 MET cc_start: 0.7011 (mmm) cc_final: 0.5253 (mtp) REVERT: A 187 THR cc_start: 0.8074 (OUTLIER) cc_final: 0.7819 (m) REVERT: A 484 MET cc_start: 0.8610 (tmm) cc_final: 0.8016 (ttt) outliers start: 6 outliers final: 2 residues processed: 28 average time/residue: 0.0887 time to fit residues: 3.1616 Evaluate side-chains 26 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 23 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 381 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 26 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 41 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.0270 chunk 3 optimal weight: 0.0020 chunk 33 optimal weight: 0.8980 overall best weight: 0.5046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.143626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.112916 restraints weight = 4210.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.116082 restraints weight = 2727.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.118177 restraints weight = 2053.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.119246 restraints weight = 1737.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.120294 restraints weight = 1569.441| |-----------------------------------------------------------------------------| r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4106 Z= 0.113 Angle : 0.503 7.227 5614 Z= 0.248 Chirality : 0.038 0.137 647 Planarity : 0.003 0.029 680 Dihedral : 5.011 30.258 591 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.45 % Allowed : 9.66 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.97 (0.38), residues: 512 helix: 1.89 (0.28), residues: 372 sheet: None (None), residues: 0 loop : -0.22 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 369 TYR 0.022 0.001 TYR A 175 PHE 0.009 0.001 PHE A 258 TRP 0.005 0.001 TRP A 141 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4106) covalent geometry : angle 0.50283 ( 5614) hydrogen bonds : bond 0.03583 ( 262) hydrogen bonds : angle 3.80568 ( 777) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.125 Fit side-chains REVERT: A 484 MET cc_start: 0.8601 (tmm) cc_final: 0.8030 (ttt) outliers start: 6 outliers final: 3 residues processed: 27 average time/residue: 0.0823 time to fit residues: 2.8364 Evaluate side-chains 27 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 24 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.141963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.111153 restraints weight = 4135.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.114194 restraints weight = 2722.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.116031 restraints weight = 2080.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.117520 restraints weight = 1763.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.118363 restraints weight = 1564.731| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.1767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4106 Z= 0.125 Angle : 0.533 8.138 5614 Z= 0.260 Chirality : 0.038 0.139 647 Planarity : 0.004 0.029 680 Dihedral : 5.222 32.726 591 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.97 % Allowed : 10.63 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.97 (0.38), residues: 512 helix: 1.90 (0.28), residues: 370 sheet: None (None), residues: 0 loop : -0.21 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 369 TYR 0.021 0.001 TYR A 175 PHE 0.010 0.001 PHE A 258 TRP 0.005 0.001 TRP A 240 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 4106) covalent geometry : angle 0.53292 ( 5614) hydrogen bonds : bond 0.03717 ( 262) hydrogen bonds : angle 3.86025 ( 777) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1024 Ramachandran restraints generated. 512 Oldfield, 0 Emsley, 512 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.105 Fit side-chains REVERT: A 139 MET cc_start: 0.6954 (mmm) cc_final: 0.5298 (ttp) REVERT: A 484 MET cc_start: 0.8603 (tmm) cc_final: 0.7880 (ttt) outliers start: 4 outliers final: 4 residues processed: 24 average time/residue: 0.0928 time to fit residues: 2.7746 Evaluate side-chains 27 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 23 time to evaluate : 0.129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 TRP Chi-restraints excluded: chain A residue 184 VAL Chi-restraints excluded: chain A residue 381 MET Chi-restraints excluded: chain A residue 399 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 51 random chunks: chunk 2 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 12 optimal weight: 0.0970 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 16 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.141311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.110593 restraints weight = 4123.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.113688 restraints weight = 2685.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.115626 restraints weight = 2048.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.117066 restraints weight = 1726.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.117706 restraints weight = 1550.775| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4106 Z= 0.126 Angle : 0.536 7.936 5614 Z= 0.261 Chirality : 0.039 0.139 647 Planarity : 0.004 0.030 680 Dihedral : 5.367 34.472 591 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.45 % Allowed : 10.14 % Favored : 88.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 1.83 (0.38), residues: 512 helix: 1.77 (0.28), residues: 373 sheet: None (None), residues: 0 loop : -0.23 (0.51), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 369 TYR 0.021 0.001 TYR A 175 PHE 0.011 0.001 PHE A 258 TRP 0.006 0.001 TRP A 141 HIS 0.002 0.000 HIS A 162 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 4106) covalent geometry : angle 0.53624 ( 5614) hydrogen bonds : bond 0.03745 ( 262) hydrogen bonds : angle 3.89139 ( 777) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 796.19 seconds wall clock time: 14 minutes 24.54 seconds (864.54 seconds total)