Starting phenix.real_space_refine on Tue Mar 3 13:43:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru6_24698/03_2026/7ru6_24698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru6_24698/03_2026/7ru6_24698.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ru6_24698/03_2026/7ru6_24698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru6_24698/03_2026/7ru6_24698.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru6_24698/03_2026/7ru6_24698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru6_24698/03_2026/7ru6_24698.cif" } resolution = 4.4 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= 0.001 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 19 5.16 5 C 1815 2.51 5 N 413 2.21 5 O 454 1.98 5 H 2725 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5426 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 5148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 5148 Classifications: {'peptide': 315} Link IDs: {'PTRANS': 8, 'TRANS': 306} Chain breaks: 4 Chain: "L" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 278 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Time building chain proxies: 1.10, per 1000 atoms: 0.20 Number of scatterers: 5426 At special positions: 0 Unit cell: (62.304, 86.966, 73.986, 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 19 16.00 O 454 8.00 N 413 7.00 C 1815 6.00 H 2725 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: 0.45 Conformation dependent library (CDL) restraints added in 252.0 milliseconds 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 630 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 1 sheets defined 86.4% alpha, 1.2% 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 34 through 57 Processing helix chain 'A' and resid 58 through 67 removed outlier: 3.635A pdb=" N GLU A 62 " --> pdb=" O ARG A 58 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N THR A 63 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR A 64 " --> pdb=" O GLU A 60 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LYS A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 116 Processing helix chain 'A' and resid 124 through 132 Processing helix chain 'A' and resid 133 through 151 removed outlier: 3.509A pdb=" N ILE A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 197 removed outlier: 3.650A pdb=" N SER A 158 " --> pdb=" O GLY A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 229 removed outlier: 3.558A pdb=" N TRP A 202 " --> pdb=" O ASN A 198 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR A 229 " --> pdb=" O TYR A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 255 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.567A pdb=" N HIS A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 289 removed outlier: 3.688A pdb=" N SER A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASN A 289 " --> pdb=" O SER A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 296 Processing helix chain 'A' and resid 335 through 353 Processing helix chain 'A' and resid 404 through 423 Processing helix chain 'A' and resid 440 through 463 Processing helix chain 'L' and resid 113 through 117 removed outlier: 3.569A pdb=" N ARG L 117 " --> pdb=" O GLY L 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'L' and resid 105 through 107 220 hydrogen bonds defined for protein. 645 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: 1.18 Time building geometry restraints manager: 0.66 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: 2718 1.03 - 1.23: 7 1.23 - 1.42: 1231 1.42 - 1.61: 1518 1.61 - 1.81: 31 Bond restraints: 5505 Sorted by residual: bond pdb=" CB TRP A 284 " pdb=" CG TRP A 284 " ideal model delta sigma weight residual 1.498 1.536 -0.038 3.10e-02 1.04e+03 1.52e+00 bond pdb=" CA TYR L 109 " pdb=" C TYR L 109 " ideal model delta sigma weight residual 1.522 1.502 0.020 1.72e-02 3.38e+03 1.29e+00 bond pdb=" N GLY A 132 " pdb=" CA GLY A 132 " ideal model delta sigma weight residual 1.442 1.450 -0.008 7.70e-03 1.69e+04 1.10e+00 bond pdb=" CB MET A 411 " pdb=" CG MET A 411 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.07e+00 bond pdb=" C TRP L 108 " pdb=" N TYR L 109 " ideal model delta sigma weight residual 1.333 1.319 0.014 1.56e-02 4.11e+03 8.31e-01 ... (remaining 5500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 9721 1.60 - 3.20: 166 3.20 - 4.80: 17 4.80 - 6.40: 4 6.40 - 8.00: 1 Bond angle restraints: 9909 Sorted by residual: angle pdb=" CB MET A 411 " pdb=" CG MET A 411 " pdb=" SD MET A 411 " ideal model delta sigma weight residual 112.70 120.70 -8.00 3.00e+00 1.11e-01 7.11e+00 angle pdb=" CA MET A 411 " pdb=" CB MET A 411 " pdb=" CG MET A 411 " ideal model delta sigma weight residual 114.10 119.04 -4.94 2.00e+00 2.50e-01 6.10e+00 angle pdb=" CA TRP A 284 " pdb=" CB TRP A 284 " pdb=" CG TRP A 284 " ideal model delta sigma weight residual 113.60 118.28 -4.68 1.90e+00 2.77e-01 6.08e+00 angle pdb=" CA MET A 105 " pdb=" CB MET A 105 " pdb=" CG MET A 105 " ideal model delta sigma weight residual 114.10 118.77 -4.67 2.00e+00 2.50e-01 5.46e+00 angle pdb=" C ILE A 55 " pdb=" N MET A 56 " pdb=" CA MET A 56 " ideal model delta sigma weight residual 120.72 117.40 3.32 1.67e+00 3.59e-01 3.95e+00 ... (remaining 9904 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.40: 2328 16.40 - 32.81: 182 32.81 - 49.21: 70 49.21 - 65.62: 19 65.62 - 82.02: 3 Dihedral angle restraints: 2602 sinusoidal: 1320 harmonic: 1282 Sorted by residual: dihedral pdb=" N LEU A 412 " pdb=" CA LEU A 412 " pdb=" CB LEU A 412 " pdb=" CG LEU A 412 " ideal model delta sinusoidal sigma weight residual -60.00 -119.36 59.36 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CB MET A 61 " pdb=" CG MET A 61 " pdb=" SD MET A 61 " pdb=" CE MET A 61 " ideal model delta sinusoidal sigma weight residual 180.00 121.39 58.61 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB GLU A 62 " pdb=" CG GLU A 62 " pdb=" CD GLU A 62 " pdb=" OE1 GLU A 62 " ideal model delta sinusoidal sigma weight residual 0.00 -82.02 82.02 1 3.00e+01 1.11e-03 9.19e+00 ... (remaining 2599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 276 0.026 - 0.052: 90 0.052 - 0.078: 45 0.078 - 0.104: 13 0.104 - 0.131: 3 Chirality restraints: 427 Sorted by residual: chirality pdb=" CA ILE A 151 " pdb=" N ILE A 151 " pdb=" C ILE A 151 " pdb=" CB ILE A 151 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.26e-01 chirality pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" C PRO A 265 " pdb=" CB PRO A 265 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA PRO A 441 " pdb=" N PRO A 441 " pdb=" C PRO A 441 " pdb=" CB PRO A 441 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 424 not shown) Planarity restraints: 757 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR L 113 " -0.004 2.00e-02 2.50e+03 5.72e-03 9.81e-01 pdb=" CG TYR L 113 " 0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR L 113 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR L 113 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR L 113 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR L 113 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR L 113 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR L 113 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 TYR L 113 " 0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR L 113 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 TYR L 113 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR L 113 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 290 " -0.016 5.00e-02 4.00e+02 2.36e-02 8.94e-01 pdb=" N PRO A 291 " 0.041 5.00e-02 4.00e+02 pdb=" CA PRO A 291 " -0.012 5.00e-02 4.00e+02 pdb=" CD PRO A 291 " -0.013 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 281 " 0.010 2.00e-02 2.50e+03 5.03e-03 7.60e-01 pdb=" CG TYR A 281 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR A 281 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 281 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 281 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 TYR A 281 " -0.000 2.00e-02 2.50e+03 pdb=" HD2 TYR A 281 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TYR A 281 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 TYR A 281 " 0.001 2.00e-02 2.50e+03 ... (remaining 754 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.19: 294 2.19 - 2.79: 10824 2.79 - 3.39: 15567 3.39 - 4.00: 18460 4.00 - 4.60: 29146 Nonbonded interactions: 74291 Sorted by model distance: nonbonded pdb=" OG SER A 285 " pdb=" HZ3 LYS A 446 " model vdw 1.583 2.450 nonbonded pdb=" O GLU A 290 " pdb="HD22 ASN A 296 " model vdw 1.632 2.450 nonbonded pdb=" O CYS A 413 " pdb=" HG SER A 416 " model vdw 1.647 2.450 nonbonded pdb=" OD1 ASP A 124 " pdb=" H ARG A 126 " model vdw 1.669 2.450 nonbonded pdb=" OE2 GLU A 195 " pdb=" H GLY L 114 " model vdw 1.682 2.450 ... (remaining 74286 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 0.690 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: 0.030 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.240 Find NCS groups from input model: 0.010 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6829 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 : 0.003 0.038 2780 Z= 0.163 Angle : 0.587 7.998 3774 Z= 0.313 Chirality : 0.035 0.131 427 Planarity : 0.003 0.031 440 Dihedral : 15.250 82.022 950 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.00 % Allowed : 22.64 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.46), residues: 319 helix: 2.60 (0.30), residues: 261 sheet: None (None), residues: 0 loop : -0.42 (0.86), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 193 TYR 0.015 0.002 TYR L 113 PHE 0.011 0.001 PHE A 110 TRP 0.014 0.001 TRP A 440 HIS 0.005 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 2780) covalent geometry : angle 0.58750 ( 3774) hydrogen bonds : bond 0.09485 ( 220) hydrogen bonds : angle 4.81837 ( 645) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1385 time to fit residues: 9.7592 Evaluate side-chains 56 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.1980 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 264 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN A 337 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.137588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.113986 restraints weight = 15002.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.118385 restraints weight = 7417.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121135 restraints weight = 4632.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.122553 restraints weight = 3377.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.123562 restraints weight = 2832.008| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2780 Z= 0.162 Angle : 0.492 5.442 3774 Z= 0.280 Chirality : 0.035 0.122 427 Planarity : 0.003 0.026 440 Dihedral : 3.540 14.414 359 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.34 % Allowed : 2.03 % Favored : 97.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.45), residues: 319 helix: 2.68 (0.29), residues: 262 sheet: None (None), residues: 0 loop : -0.23 (0.86), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 126 TYR 0.024 0.001 TYR A 281 PHE 0.011 0.001 PHE A 112 TRP 0.017 0.001 TRP A 284 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2780) covalent geometry : angle 0.49235 ( 3774) hydrogen bonds : bond 0.04588 ( 220) hydrogen bonds : angle 3.95294 ( 645) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.7144 (mm) cc_final: 0.6858 (mm) REVERT: A 175 GLN cc_start: 0.8830 (OUTLIER) cc_final: 0.8554 (tm-30) REVERT: A 188 GLU cc_start: 0.8660 (tt0) cc_final: 0.8176 (mt-10) REVERT: A 226 THR cc_start: 0.7546 (m) cc_final: 0.7333 (m) REVERT: A 411 MET cc_start: 0.8627 (tmm) cc_final: 0.8144 (tmm) outliers start: 1 outliers final: 0 residues processed: 71 average time/residue: 0.1422 time to fit residues: 11.8810 Evaluate side-chains 61 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 6 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 289 ASN A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.136525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.114646 restraints weight = 15103.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.118935 restraints weight = 7499.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.121281 restraints weight = 4644.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.122901 restraints weight = 3457.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.123585 restraints weight = 2814.711| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 2780 Z= 0.133 Angle : 0.475 4.992 3774 Z= 0.265 Chirality : 0.033 0.116 427 Planarity : 0.003 0.025 440 Dihedral : 3.467 14.840 359 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.44), residues: 319 helix: 2.94 (0.29), residues: 262 sheet: None (None), residues: 0 loop : -0.14 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 193 TYR 0.020 0.002 TYR A 281 PHE 0.009 0.001 PHE A 112 TRP 0.008 0.001 TRP L 108 HIS 0.007 0.002 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 2780) covalent geometry : angle 0.47477 ( 3774) hydrogen bonds : bond 0.04330 ( 220) hydrogen bonds : angle 3.75035 ( 645) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 THR cc_start: 0.7470 (m) cc_final: 0.7269 (m) REVERT: A 409 HIS cc_start: 0.7894 (m-70) cc_final: 0.7675 (m-70) REVERT: A 411 MET cc_start: 0.8536 (tmm) cc_final: 0.7974 (tmm) REVERT: A 453 CYS cc_start: 0.9035 (t) cc_final: 0.8795 (t) REVERT: L 107 SER cc_start: 0.9346 (m) cc_final: 0.8630 (p) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.1382 time to fit residues: 11.0625 Evaluate side-chains 58 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.134753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.112942 restraints weight = 15293.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117347 restraints weight = 7335.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119877 restraints weight = 4466.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.121517 restraints weight = 3254.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.122274 restraints weight = 2617.252| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2780 Z= 0.162 Angle : 0.492 5.091 3774 Z= 0.275 Chirality : 0.034 0.123 427 Planarity : 0.003 0.024 440 Dihedral : 3.498 15.066 359 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.34 % Allowed : 1.35 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.68 (0.44), residues: 319 helix: 2.92 (0.28), residues: 264 sheet: None (None), residues: 0 loop : -0.17 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 39 TYR 0.021 0.002 TYR A 225 PHE 0.008 0.001 PHE A 110 TRP 0.006 0.001 TRP A 202 HIS 0.005 0.002 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 2780) covalent geometry : angle 0.49231 ( 3774) hydrogen bonds : bond 0.04185 ( 220) hydrogen bonds : angle 3.80719 ( 645) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 68 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 188 GLU cc_start: 0.8683 (tt0) cc_final: 0.8341 (tm-30) REVERT: A 226 THR cc_start: 0.7662 (m) cc_final: 0.7408 (m) REVERT: A 411 MET cc_start: 0.8556 (tmm) cc_final: 0.8045 (tmm) REVERT: A 453 CYS cc_start: 0.9025 (t) cc_final: 0.8607 (t) outliers start: 1 outliers final: 0 residues processed: 69 average time/residue: 0.1357 time to fit residues: 11.2244 Evaluate side-chains 55 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.132931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.111969 restraints weight = 15464.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.116135 restraints weight = 7530.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.118572 restraints weight = 4575.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.119428 restraints weight = 3318.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.120417 restraints weight = 2890.753| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7151 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2780 Z= 0.167 Angle : 0.496 4.765 3774 Z= 0.276 Chirality : 0.034 0.124 427 Planarity : 0.003 0.025 440 Dihedral : 3.521 15.566 359 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.34 % Allowed : 3.38 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.60 (0.44), residues: 319 helix: 2.88 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.28 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.018 0.002 TYR A 281 PHE 0.008 0.001 PHE A 213 TRP 0.005 0.001 TRP A 284 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2780) covalent geometry : angle 0.49635 ( 3774) hydrogen bonds : bond 0.04210 ( 220) hydrogen bonds : angle 3.81152 ( 645) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.6982 (mm) cc_final: 0.6711 (mm) REVERT: A 188 GLU cc_start: 0.8594 (tt0) cc_final: 0.8171 (mt-10) REVERT: A 226 THR cc_start: 0.7704 (m) cc_final: 0.7480 (m) REVERT: A 411 MET cc_start: 0.8522 (tmm) cc_final: 0.8059 (tmm) REVERT: A 453 CYS cc_start: 0.8897 (t) cc_final: 0.8549 (t) REVERT: L 107 SER cc_start: 0.9318 (m) cc_final: 0.8622 (p) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.1475 time to fit residues: 11.8957 Evaluate side-chains 55 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 28 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 289 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.133008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.112161 restraints weight = 15543.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.116230 restraints weight = 7868.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.118689 restraints weight = 4911.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.119933 restraints weight = 3614.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.120852 restraints weight = 3039.832| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2780 Z= 0.167 Angle : 0.504 4.509 3774 Z= 0.281 Chirality : 0.035 0.122 427 Planarity : 0.003 0.025 440 Dihedral : 3.487 15.205 359 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.34 % Allowed : 0.34 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.51 (0.44), residues: 319 helix: 2.81 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.27 (0.84), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 193 TYR 0.017 0.002 TYR A 281 PHE 0.009 0.001 PHE A 209 TRP 0.006 0.001 TRP L 115 HIS 0.004 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00330 ( 2780) covalent geometry : angle 0.50442 ( 3774) hydrogen bonds : bond 0.04206 ( 220) hydrogen bonds : angle 3.81997 ( 645) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8148 (pt) cc_final: 0.7911 (pt) REVERT: A 188 GLU cc_start: 0.8570 (tt0) cc_final: 0.8129 (mt-10) REVERT: A 226 THR cc_start: 0.7622 (m) cc_final: 0.7414 (m) REVERT: A 411 MET cc_start: 0.8488 (tmm) cc_final: 0.8071 (tmm) REVERT: A 453 CYS cc_start: 0.8886 (t) cc_final: 0.8496 (t) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.1500 time to fit residues: 12.6827 Evaluate side-chains 56 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 13 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 0.0670 chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.132964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.111968 restraints weight = 15425.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116193 restraints weight = 7547.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.118719 restraints weight = 4629.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.120165 restraints weight = 3327.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121089 restraints weight = 2706.663| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.3963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2780 Z= 0.140 Angle : 0.483 4.881 3774 Z= 0.263 Chirality : 0.034 0.117 427 Planarity : 0.003 0.026 440 Dihedral : 3.413 15.313 359 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.76 (0.44), residues: 319 helix: 3.01 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.35 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 193 TYR 0.016 0.001 TYR A 281 PHE 0.007 0.001 PHE A 209 TRP 0.006 0.001 TRP L 115 HIS 0.003 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 2780) covalent geometry : angle 0.48314 ( 3774) hydrogen bonds : bond 0.04138 ( 220) hydrogen bonds : angle 3.68179 ( 645) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.136 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8134 (pt) cc_final: 0.7910 (pt) REVERT: A 226 THR cc_start: 0.7611 (m) cc_final: 0.7401 (m) REVERT: A 411 MET cc_start: 0.8416 (tmm) cc_final: 0.8025 (tmm) REVERT: A 453 CYS cc_start: 0.8794 (t) cc_final: 0.8425 (t) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1239 time to fit residues: 10.0971 Evaluate side-chains 55 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 0.0000 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 2 optimal weight: 0.0770 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 0.3980 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 0.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.134999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113649 restraints weight = 15065.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.117984 restraints weight = 7311.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.120548 restraints weight = 4390.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.121853 restraints weight = 3140.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.122798 restraints weight = 2605.023| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7098 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 2780 Z= 0.110 Angle : 0.458 5.234 3774 Z= 0.243 Chirality : 0.033 0.109 427 Planarity : 0.003 0.028 440 Dihedral : 3.378 15.340 359 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.01 (0.45), residues: 319 helix: 3.17 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.16 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.013 0.001 TYR A 281 PHE 0.005 0.001 PHE A 209 TRP 0.007 0.001 TRP A 190 HIS 0.007 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00221 ( 2780) covalent geometry : angle 0.45817 ( 3774) hydrogen bonds : bond 0.04023 ( 220) hydrogen bonds : angle 3.53521 ( 645) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 166 ILE cc_start: 0.8091 (pt) cc_final: 0.7852 (pt) REVERT: A 226 THR cc_start: 0.7564 (m) cc_final: 0.7348 (m) REVERT: A 411 MET cc_start: 0.8415 (tmm) cc_final: 0.8084 (tmm) REVERT: A 453 CYS cc_start: 0.8866 (t) cc_final: 0.8439 (t) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.1290 time to fit residues: 11.0380 Evaluate side-chains 59 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 0.0980 chunk 20 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 12 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.134025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.112846 restraints weight = 15102.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117108 restraints weight = 7287.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.119705 restraints weight = 4417.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.121215 restraints weight = 3158.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.121942 restraints weight = 2530.740| |-----------------------------------------------------------------------------| r_work (final): 0.3672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 2780 Z= 0.124 Angle : 0.449 5.191 3774 Z= 0.245 Chirality : 0.033 0.117 427 Planarity : 0.003 0.027 440 Dihedral : 3.381 15.364 359 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.97 (0.44), residues: 319 helix: 3.13 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.08 (0.84), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 193 TYR 0.013 0.001 TYR A 281 PHE 0.009 0.001 PHE A 110 TRP 0.006 0.001 TRP L 115 HIS 0.006 0.001 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 2780) covalent geometry : angle 0.44907 ( 3774) hydrogen bonds : bond 0.03996 ( 220) hydrogen bonds : angle 3.56914 ( 645) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 ILE cc_start: 0.6944 (mm) cc_final: 0.6651 (mm) REVERT: A 166 ILE cc_start: 0.8073 (pt) cc_final: 0.7846 (pt) REVERT: A 411 MET cc_start: 0.8424 (tmm) cc_final: 0.8009 (tmm) REVERT: A 453 CYS cc_start: 0.8868 (t) cc_final: 0.8498 (t) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.1349 time to fit residues: 11.3772 Evaluate side-chains 56 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 21 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 23 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.131114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.109681 restraints weight = 15577.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.113881 restraints weight = 7539.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.116282 restraints weight = 4589.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.117869 restraints weight = 3349.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.118598 restraints weight = 2677.069| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.4344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2780 Z= 0.178 Angle : 0.510 4.953 3774 Z= 0.286 Chirality : 0.034 0.127 427 Planarity : 0.003 0.025 440 Dihedral : 3.520 15.164 359 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.44), residues: 319 helix: 2.82 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.39 (0.84), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 200 TYR 0.015 0.002 TYR A 281 PHE 0.007 0.001 PHE A 213 TRP 0.007 0.001 TRP L 115 HIS 0.012 0.002 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 2780) covalent geometry : angle 0.51026 ( 3774) hydrogen bonds : bond 0.04153 ( 220) hydrogen bonds : angle 3.80659 ( 645) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 638 Ramachandran restraints generated. 319 Oldfield, 0 Emsley, 319 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 226 THR cc_start: 0.7667 (m) cc_final: 0.7453 (m) REVERT: A 411 MET cc_start: 0.8431 (tmm) cc_final: 0.8034 (tmm) REVERT: A 453 CYS cc_start: 0.8874 (t) cc_final: 0.8501 (t) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1284 time to fit residues: 10.6935 Evaluate side-chains 57 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 9 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 237 ASN A 409 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.132161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.110055 restraints weight = 15414.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.114374 restraints weight = 7483.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117016 restraints weight = 4555.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118302 restraints weight = 3257.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.119049 restraints weight = 2704.563| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2780 Z= 0.134 Angle : 0.484 5.169 3774 Z= 0.261 Chirality : 0.034 0.121 427 Planarity : 0.004 0.026 440 Dihedral : 3.473 14.318 359 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.69 (0.44), residues: 319 helix: 2.96 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.36 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 266 TYR 0.013 0.001 TYR A 281 PHE 0.009 0.001 PHE A 110 TRP 0.007 0.001 TRP L 115 HIS 0.008 0.002 HIS A 130 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 2780) covalent geometry : angle 0.48414 ( 3774) hydrogen bonds : bond 0.04051 ( 220) hydrogen bonds : angle 3.64058 ( 645) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1457.22 seconds wall clock time: 25 minutes 24.20 seconds (1524.20 seconds total)