Starting phenix.real_space_refine on Fri Aug 22 18:43:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ubw_42107/08_2025/8ubw_42107_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ubw_42107/08_2025/8ubw_42107.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ubw_42107/08_2025/8ubw_42107.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ubw_42107/08_2025/8ubw_42107.map" model { file = "/net/cci-nas-00/data/ceres_data/8ubw_42107/08_2025/8ubw_42107_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ubw_42107/08_2025/8ubw_42107_trim.cif" } resolution = 2.59 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= 0.025 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 S 18 5.16 5 C 2259 2.51 5 N 502 2.21 5 O 619 1.98 5 H 3343 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6741 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 6591 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 6591 Classifications: {'peptide': 418} Link IDs: {'PTRANS': 17, 'TRANS': 400} Chain: "A" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 150 Unusual residues: {'CHT': 1, 'Y01': 3} Classifications: {'undetermined': 4, 'water': 38} Link IDs: {None: 41} Time building chain proxies: 1.66, per 1000 atoms: 0.25 Number of scatterers: 6741 At special positions: 0 Unit cell: (84.1, 55.1, 65.975, 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 18 16.00 O 619 8.00 N 502 7.00 C 2259 6.00 H 3343 1.00 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: 0.66 Conformation dependent library (CDL) restraints added in 308.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 766 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 89.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.17 Creating SS restraints... Processing helix chain 'A' and resid 105 through 131 removed outlier: 3.981A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE A 114 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 5.186A pdb=" N TYR A 128 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N SER A 129 " --> pdb=" O TRP A 125 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ILE A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 Processing helix chain 'A' and resid 142 through 172 removed outlier: 3.730A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL A 158 " --> pdb=" O MET A 154 " (cutoff:3.500A) Proline residue: A 159 - end of helix removed outlier: 5.021A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.870A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 215 removed outlier: 3.649A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.244A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.512A pdb=" N ASN A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 314 Processing helix chain 'A' and resid 320 through 330 Processing helix chain 'A' and resid 331 through 363 removed outlier: 5.147A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.451A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 396 Processing helix chain 'A' and resid 397 through 420 Processing helix chain 'A' and resid 421 through 423 No H-bonds generated for 'chain 'A' and resid 421 through 423' Processing helix chain 'A' and resid 424 through 454 removed outlier: 3.500A pdb=" N VAL A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N LEU A 443 " --> pdb=" O MET A 439 " (cutoff:3.500A) Proline residue: A 444 - end of helix Processing helix chain 'A' and resid 458 through 488 removed outlier: 3.516A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.868A pdb=" N GLY A 493 " --> pdb=" O GLY A 489 " (cutoff:3.500A) 272 hydrogen bonds defined for protein. 816 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: 1.55 Time building geometry restraints manager: 0.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3335 1.03 - 1.23: 11 1.23 - 1.42: 1394 1.42 - 1.62: 2026 1.62 - 1.81: 28 Bond restraints: 6794 Sorted by residual: bond pdb=" N VAL A 195 " pdb=" CA VAL A 195 " ideal model delta sigma weight residual 1.474 1.459 0.016 1.57e-02 4.06e+03 1.01e+00 bond pdb=" CB ASN A 265 " pdb=" CG ASN A 265 " ideal model delta sigma weight residual 1.516 1.536 -0.020 2.50e-02 1.60e+03 6.57e-01 bond pdb=" C VAL A 260 " pdb=" O VAL A 260 " ideal model delta sigma weight residual 1.232 1.240 -0.008 1.01e-02 9.80e+03 6.33e-01 bond pdb=" N VAL A 260 " pdb=" CA VAL A 260 " ideal model delta sigma weight residual 1.456 1.462 -0.006 8.60e-03 1.35e+04 4.35e-01 bond pdb=" CB ASN A 331 " pdb=" CG ASN A 331 " ideal model delta sigma weight residual 1.516 1.532 -0.016 2.50e-02 1.60e+03 3.86e-01 ... (remaining 6789 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 11326 0.99 - 1.99: 890 1.99 - 2.98: 33 2.98 - 3.98: 16 3.98 - 4.97: 5 Bond angle restraints: 12270 Sorted by residual: angle pdb=" N VAL A 195 " pdb=" CA VAL A 195 " pdb=" C VAL A 195 " ideal model delta sigma weight residual 106.21 109.73 -3.52 1.07e+00 8.73e-01 1.08e+01 angle pdb=" C ILE A 332 " pdb=" CA ILE A 332 " pdb=" CB ILE A 332 " ideal model delta sigma weight residual 114.00 110.64 3.36 1.31e+00 5.83e-01 6.57e+00 angle pdb=" C ASN A 331 " pdb=" N ILE A 332 " pdb=" CA ILE A 332 " ideal model delta sigma weight residual 120.33 122.28 -1.95 8.00e-01 1.56e+00 5.95e+00 angle pdb=" C VAL A 195 " pdb=" CA VAL A 195 " pdb=" CB VAL A 195 " ideal model delta sigma weight residual 113.22 110.82 2.40 1.12e+00 7.97e-01 4.60e+00 angle pdb=" CA VAL A 195 " pdb=" C VAL A 195 " pdb=" O VAL A 195 " ideal model delta sigma weight residual 122.63 120.87 1.76 8.70e-01 1.32e+00 4.08e+00 ... (remaining 12265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 3034 17.95 - 35.91: 200 35.91 - 53.86: 100 53.86 - 71.82: 29 71.82 - 89.77: 3 Dihedral angle restraints: 3366 sinusoidal: 1889 harmonic: 1477 Sorted by residual: dihedral pdb=" CA LEU A 254 " pdb=" C LEU A 254 " pdb=" N LEU A 255 " pdb=" CA LEU A 255 " ideal model delta harmonic sigma weight residual 180.00 -163.65 -16.35 0 5.00e+00 4.00e-02 1.07e+01 dihedral pdb=" CB MET A 358 " pdb=" CG MET A 358 " pdb=" SD MET A 358 " pdb=" CE MET A 358 " ideal model delta sinusoidal sigma weight residual 60.00 5.96 54.04 3 1.50e+01 4.44e-03 9.25e+00 dihedral pdb=" CA ARG A 372 " pdb=" CB ARG A 372 " pdb=" CG ARG A 372 " pdb=" CD ARG A 372 " ideal model delta sinusoidal sigma weight residual -180.00 -129.13 -50.87 3 1.50e+01 4.44e-03 8.95e+00 ... (remaining 3363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.023: 374 0.023 - 0.045: 103 0.045 - 0.067: 44 0.067 - 0.090: 38 0.090 - 0.112: 9 Chirality restraints: 568 Sorted by residual: chirality pdb=" CA PRO A 333 " pdb=" N PRO A 333 " pdb=" C PRO A 333 " pdb=" CB PRO A 333 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.16e-01 chirality pdb=" CA ASN A 331 " pdb=" N ASN A 331 " pdb=" C ASN A 331 " pdb=" CB ASN A 331 " both_signs ideal model delta sigma weight residual False 2.51 2.62 -0.11 2.00e-01 2.50e+01 3.12e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.00e-01 ... (remaining 565 not shown) Planarity restraints: 957 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 114 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.58e+00 pdb=" C PHE A 114 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE A 114 " 0.010 2.00e-02 2.50e+03 pdb=" N SER A 115 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 230 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.37e+00 pdb=" N PRO A 231 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 231 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 231 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 331 " -0.005 2.00e-02 2.50e+03 9.06e-03 1.23e+00 pdb=" CG ASN A 331 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 331 " -0.009 2.00e-02 2.50e+03 pdb=" ND2 ASN A 331 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN A 331 " -0.003 2.00e-02 2.50e+03 pdb="HD22 ASN A 331 " -0.001 2.00e-02 2.50e+03 ... (remaining 954 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 931 2.26 - 2.85: 15618 2.85 - 3.43: 18994 3.43 - 4.02: 25823 4.02 - 4.60: 39249 Nonbonded interactions: 100615 Sorted by model distance: nonbonded pdb=" O ILE A 415 " pdb=" HG1 THR A 419 " model vdw 1.679 2.450 nonbonded pdb=" HG SER A 350 " pdb=" OE1 GLN A 481 " model vdw 1.699 2.450 nonbonded pdb=" HH TYR A 349 " pdb=" O HOH A 702 " model vdw 1.736 2.450 nonbonded pdb=" HH TYR A 139 " pdb=" O SER A 194 " model vdw 1.750 2.450 nonbonded pdb=" H GLY A 219 " pdb=" O HOH A 707 " model vdw 1.762 2.450 ... (remaining 100610 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 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: 5.370 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: 0.060 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.020 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3451 Z= 0.111 Angle : 0.476 4.974 4724 Z= 0.269 Chirality : 0.033 0.112 568 Planarity : 0.003 0.029 557 Dihedral : 14.624 89.769 1369 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.85 % Allowed : 14.41 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.39 (0.42), residues: 416 helix: 3.09 (0.28), residues: 334 sheet: None (None), residues: 0 loop : -1.68 (0.55), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 171 TYR 0.015 0.001 TYR A 117 PHE 0.012 0.001 PHE A 496 TRP 0.003 0.001 TRP A 201 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00205 ( 3451) covalent geometry : angle 0.47559 ( 4724) hydrogen bonds : bond 0.11398 ( 272) hydrogen bonds : angle 5.51381 ( 816) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 44 time to evaluate : 0.183 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.7974 (m-80) cc_final: 0.7672 (m-80) REVERT: A 459 GLU cc_start: 0.7166 (tm-30) cc_final: 0.6840 (tm-30) outliers start: 3 outliers final: 1 residues processed: 46 average time/residue: 1.3125 time to fit residues: 62.1736 Evaluate side-chains 34 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN A 264 GLN A 331 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.097875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.078873 restraints weight = 16186.102| |-----------------------------------------------------------------------------| r_work (start): 0.2954 rms_B_bonded: 2.11 r_work: 0.2859 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3451 Z= 0.169 Angle : 0.510 5.638 4724 Z= 0.270 Chirality : 0.035 0.123 568 Planarity : 0.004 0.031 557 Dihedral : 5.723 54.258 664 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.41 % Allowed : 14.69 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.62 (0.40), residues: 416 helix: 3.12 (0.27), residues: 341 sheet: None (None), residues: 0 loop : -1.36 (0.60), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 223 TYR 0.023 0.001 TYR A 117 PHE 0.016 0.001 PHE A 496 TRP 0.005 0.001 TRP A 201 HIS 0.000 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 3451) covalent geometry : angle 0.51036 ( 4724) hydrogen bonds : bond 0.05199 ( 272) hydrogen bonds : angle 4.38385 ( 816) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8219 (m-80) cc_final: 0.7858 (m-80) REVERT: A 459 GLU cc_start: 0.7240 (tm-30) cc_final: 0.6801 (tm-30) outliers start: 5 outliers final: 1 residues processed: 36 average time/residue: 1.3788 time to fit residues: 51.1932 Evaluate side-chains 30 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 6 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.0980 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.095563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.076991 restraints weight = 16178.629| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.09 r_work: 0.2854 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3451 Z= 0.147 Angle : 0.478 4.945 4724 Z= 0.253 Chirality : 0.034 0.119 568 Planarity : 0.004 0.029 557 Dihedral : 5.643 51.659 664 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.66 (0.40), residues: 416 helix: 3.09 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.49 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 223 TYR 0.023 0.001 TYR A 117 PHE 0.014 0.001 PHE A 496 TRP 0.006 0.001 TRP A 201 HIS 0.000 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 3451) covalent geometry : angle 0.47785 ( 4724) hydrogen bonds : bond 0.04958 ( 272) hydrogen bonds : angle 4.21172 ( 816) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.235 Fit side-chains revert: symmetry clash REVERT: A 302 TYR cc_start: 0.8272 (m-80) cc_final: 0.7892 (m-80) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.9605 time to fit residues: 28.1631 Evaluate side-chains 25 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 37 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 overall best weight: 0.4178 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.096199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.077398 restraints weight = 16352.203| |-----------------------------------------------------------------------------| r_work (start): 0.2955 rms_B_bonded: 2.13 r_work: 0.2859 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3451 Z= 0.120 Angle : 0.462 5.122 4724 Z= 0.244 Chirality : 0.034 0.119 568 Planarity : 0.004 0.029 557 Dihedral : 5.245 49.801 662 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 0.00 % Allowed : 16.38 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.80 (0.40), residues: 416 helix: 3.17 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.38 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 223 TYR 0.022 0.001 TYR A 117 PHE 0.013 0.001 PHE A 496 TRP 0.005 0.001 TRP A 201 HIS 0.000 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 3451) covalent geometry : angle 0.46174 ( 4724) hydrogen bonds : bond 0.04496 ( 272) hydrogen bonds : angle 4.06479 ( 816) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.199 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 27 average time/residue: 0.8616 time to fit residues: 24.5216 Evaluate side-chains 26 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 243 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 3 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 5 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.0270 chunk 20 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 0.0060 overall best weight: 0.4454 ------------------------------------------------------------------------------- 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 = 0.3267 r_free = 0.3267 target = 0.095412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.076881 restraints weight = 16490.029| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.12 r_work: 0.2851 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3451 Z= 0.121 Angle : 0.454 5.103 4724 Z= 0.241 Chirality : 0.034 0.121 568 Planarity : 0.004 0.030 557 Dihedral : 5.138 46.950 662 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.56 % Allowed : 16.10 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.86 (0.41), residues: 416 helix: 3.24 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.51 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 223 TYR 0.023 0.001 TYR A 117 PHE 0.013 0.001 PHE A 496 TRP 0.004 0.001 TRP A 201 HIS 0.000 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3451) covalent geometry : angle 0.45405 ( 4724) hydrogen bonds : bond 0.04491 ( 272) hydrogen bonds : angle 4.01294 ( 816) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.9400 time to fit residues: 27.5532 Evaluate side-chains 27 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3235 r_free = 0.3235 target = 0.093169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.074691 restraints weight = 16514.527| |-----------------------------------------------------------------------------| r_work (start): 0.2884 rms_B_bonded: 2.09 r_work: 0.2783 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2681 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3451 Z= 0.159 Angle : 0.481 5.414 4724 Z= 0.257 Chirality : 0.035 0.128 568 Planarity : 0.004 0.037 557 Dihedral : 5.296 43.281 662 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.28 % Allowed : 16.10 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.76 (0.41), residues: 416 helix: 3.18 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.65 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 301 TYR 0.023 0.001 TYR A 117 PHE 0.015 0.001 PHE A 496 TRP 0.005 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 3451) covalent geometry : angle 0.48105 ( 4724) hydrogen bonds : bond 0.04898 ( 272) hydrogen bonds : angle 4.08487 ( 816) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.186 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 30 average time/residue: 0.9453 time to fit residues: 29.7073 Evaluate side-chains 27 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 16 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 29 optimal weight: 2.9990 chunk 15 optimal weight: 0.0770 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.3696 ------------------------------------------------------------------------------- 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 = 0.3260 r_free = 0.3260 target = 0.094842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.076333 restraints weight = 16239.998| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.10 r_work: 0.2823 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3451 Z= 0.114 Angle : 0.455 5.140 4724 Z= 0.242 Chirality : 0.034 0.121 568 Planarity : 0.004 0.029 557 Dihedral : 5.071 41.867 662 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.28 % Allowed : 16.67 % Favored : 83.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.86 (0.41), residues: 416 helix: 3.26 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.68 (0.63), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 301 TYR 0.022 0.001 TYR A 117 PHE 0.012 0.001 PHE A 496 TRP 0.006 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 3451) covalent geometry : angle 0.45541 ( 4724) hydrogen bonds : bond 0.04431 ( 272) hydrogen bonds : angle 3.97490 ( 816) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.9222 time to fit residues: 27.0721 Evaluate side-chains 28 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 38 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 20 optimal weight: 0.3980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 3 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3227 r_free = 0.3227 target = 0.092543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.074049 restraints weight = 16495.627| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.10 r_work: 0.2807 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3451 Z= 0.155 Angle : 0.481 5.473 4724 Z= 0.257 Chirality : 0.035 0.128 568 Planarity : 0.004 0.031 557 Dihedral : 5.171 37.644 662 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.56 % Allowed : 16.10 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.77 (0.41), residues: 416 helix: 3.20 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.69 (0.64), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 107 TYR 0.024 0.001 TYR A 117 PHE 0.015 0.001 PHE A 496 TRP 0.005 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 3451) covalent geometry : angle 0.48089 ( 4724) hydrogen bonds : bond 0.04870 ( 272) hydrogen bonds : angle 4.06308 ( 816) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 29 average time/residue: 0.7897 time to fit residues: 23.9222 Evaluate side-chains 27 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 27 optimal weight: 0.3980 chunk 21 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- 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 = 0.3236 r_free = 0.3236 target = 0.093096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.074656 restraints weight = 16653.466| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.11 r_work: 0.2810 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3451 Z= 0.140 Angle : 0.478 5.314 4724 Z= 0.255 Chirality : 0.034 0.126 568 Planarity : 0.005 0.052 557 Dihedral : 5.129 36.073 662 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.28 % Allowed : 16.10 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.79 (0.41), residues: 416 helix: 3.21 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.71 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 301 TYR 0.022 0.001 TYR A 117 PHE 0.014 0.001 PHE A 496 TRP 0.006 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 3451) covalent geometry : angle 0.47829 ( 4724) hydrogen bonds : bond 0.04733 ( 272) hydrogen bonds : angle 4.03438 ( 816) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.175 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.9909 time to fit residues: 29.0045 Evaluate side-chains 27 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 8 optimal weight: 0.9990 chunk 20 optimal weight: 0.0970 chunk 18 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- 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 = 0.3239 r_free = 0.3239 target = 0.093247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.074906 restraints weight = 16559.103| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 2.09 r_work: 0.2820 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3451 Z= 0.132 Angle : 0.466 5.321 4724 Z= 0.248 Chirality : 0.034 0.125 568 Planarity : 0.004 0.030 557 Dihedral : 5.097 35.095 662 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.28 % Allowed : 16.10 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.79 (0.41), residues: 416 helix: 3.22 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.75 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 301 TYR 0.023 0.001 TYR A 117 PHE 0.013 0.001 PHE A 496 TRP 0.006 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3451) covalent geometry : angle 0.46562 ( 4724) hydrogen bonds : bond 0.04648 ( 272) hydrogen bonds : angle 4.01313 ( 816) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 832 Ramachandran restraints generated. 416 Oldfield, 0 Emsley, 416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.8099 time to fit residues: 23.7960 Evaluate side-chains 27 residues out of total 354 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3225 r_free = 0.3225 target = 0.092318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.074002 restraints weight = 16503.278| |-----------------------------------------------------------------------------| r_work (start): 0.2872 rms_B_bonded: 2.08 r_work: 0.2770 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2667 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3451 Z= 0.153 Angle : 0.484 5.418 4724 Z= 0.259 Chirality : 0.035 0.128 568 Planarity : 0.004 0.032 557 Dihedral : 5.177 33.967 662 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 0.28 % Allowed : 16.38 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 3.74 (0.41), residues: 416 helix: 3.19 (0.27), residues: 348 sheet: None (None), residues: 0 loop : -1.77 (0.65), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 301 TYR 0.023 0.001 TYR A 117 PHE 0.015 0.001 PHE A 496 TRP 0.005 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 3451) covalent geometry : angle 0.48391 ( 4724) hydrogen bonds : bond 0.04844 ( 272) hydrogen bonds : angle 4.05794 ( 816) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2626.00 seconds wall clock time: 45 minutes 22.08 seconds (2722.08 seconds total)