Starting phenix.real_space_refine on Thu Mar 6 08:06:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru6_24698/03_2025/7ru6_24698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru6_24698/03_2025/7ru6_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_2025/7ru6_24698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru6_24698/03_2025/7ru6_24698.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru6_24698/03_2025/7ru6_24698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru6_24698/03_2025/7ru6_24698.cif" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 3.24, per 1000 atoms: 0.60 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: 1.52 Conformation dependent library (CDL) restraints added in 496.2 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: 0.40 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: 1.81 Time building geometry restraints manager: 1.75 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: 0.540 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: 0.090 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.530 Find NCS groups from input model: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.430 ------------------------------------------------------------------------------- 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= 0.218 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (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 TRP 0.014 0.001 TRP A 440 HIS 0.005 0.001 HIS A 130 PHE 0.011 0.001 PHE A 110 TYR 0.015 0.002 TYR L 113 ARG 0.001 0.000 ARG A 193 *********************** 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 : 0.375 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: 0.2989 time to fit residues: 21.1500 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 : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 9 optimal weight: 0.1980 chunk 15 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 A 289 ASN A 337 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.138293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114804 restraints weight = 14843.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.119188 restraints weight = 7373.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.121895 restraints weight = 4640.154| |-----------------------------------------------------------------------------| r_work (final): 0.3670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2780 Z= 0.192 Angle : 0.483 5.337 3774 Z= 0.274 Chirality : 0.034 0.120 427 Planarity : 0.003 0.026 440 Dihedral : 3.506 14.334 359 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Rotamer: Outliers : 0.34 % Allowed : 1.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.38 (0.45), residues: 319 helix: 2.72 (0.29), residues: 262 sheet: None (None), residues: 0 loop : -0.18 (0.86), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 284 HIS 0.004 0.001 HIS A 130 PHE 0.012 0.001 PHE A 112 TYR 0.024 0.001 TYR A 281 ARG 0.002 0.000 ARG A 126 *********************** 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 72 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.370 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: 0.7110 (mm) cc_final: 0.6846 (mm) REVERT: A 175 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8526 (tm-30) REVERT: A 226 THR cc_start: 0.7547 (m) cc_final: 0.7329 (m) REVERT: A 411 MET cc_start: 0.8631 (tmm) cc_final: 0.8157 (tmm) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.3247 time to fit residues: 27.6003 Evaluate side-chains 62 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 61 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 12 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.135640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114348 restraints weight = 15216.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.118161 restraints weight = 7925.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.120470 restraints weight = 5116.430| |-----------------------------------------------------------------------------| r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.2934 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= 0.195 Angle : 0.488 4.984 3774 Z= 0.274 Chirality : 0.034 0.120 427 Planarity : 0.003 0.024 440 Dihedral : 3.496 14.943 359 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.00 % Allowed : 2.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.44), residues: 319 helix: 2.83 (0.29), residues: 262 sheet: None (None), residues: 0 loop : -0.09 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP L 108 HIS 0.007 0.001 HIS A 130 PHE 0.012 0.001 PHE A 112 TYR 0.020 0.002 TYR A 278 ARG 0.001 0.000 ARG A 193 *********************** 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 68 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.373 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 188 GLU cc_start: 0.8633 (tt0) cc_final: 0.8280 (mt-10) REVERT: A 226 THR cc_start: 0.7450 (m) cc_final: 0.7246 (m) REVERT: A 411 MET cc_start: 0.8577 (tmm) cc_final: 0.8049 (tmm) REVERT: A 453 CYS cc_start: 0.8911 (t) cc_final: 0.8676 (t) REVERT: L 107 SER cc_start: 0.9318 (m) cc_final: 0.8729 (p) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2877 time to fit residues: 23.6663 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 : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 24 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 22 optimal weight: 0.3980 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.134751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.112649 restraints weight = 15563.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.117024 restraints weight = 7495.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.119491 restraints weight = 4576.810| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2780 Z= 0.204 Angle : 0.486 5.016 3774 Z= 0.270 Chirality : 0.034 0.121 427 Planarity : 0.003 0.025 440 Dihedral : 3.487 15.162 359 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.82 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.68 (0.43), residues: 319 helix: 2.91 (0.28), residues: 264 sheet: None (None), residues: 0 loop : -0.13 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.005 0.002 HIS A 130 PHE 0.010 0.001 PHE A 112 TYR 0.021 0.002 TYR A 225 ARG 0.001 0.000 ARG A 58 *********************** 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 67 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.434 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 188 GLU cc_start: 0.8693 (tt0) cc_final: 0.8378 (tm-30) REVERT: A 226 THR cc_start: 0.7635 (m) cc_final: 0.7400 (m) REVERT: A 411 MET cc_start: 0.8551 (tmm) cc_final: 0.8023 (tmm) REVERT: A 453 CYS cc_start: 0.8949 (t) cc_final: 0.8530 (t) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.2967 time to fit residues: 24.0999 Evaluate side-chains 54 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 8 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.134583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.113377 restraints weight = 15446.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.117668 restraints weight = 7448.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.119920 restraints weight = 4547.080| |-----------------------------------------------------------------------------| r_work (final): 0.3640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2780 Z= 0.174 Angle : 0.467 4.462 3774 Z= 0.257 Chirality : 0.033 0.115 427 Planarity : 0.003 0.026 440 Dihedral : 3.444 15.500 359 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.83 (0.44), residues: 319 helix: 3.02 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.09 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 190 HIS 0.003 0.001 HIS A 130 PHE 0.010 0.001 PHE A 112 TYR 0.018 0.001 TYR A 281 ARG 0.001 0.000 ARG L 117 *********************** 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 67 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 66 time to evaluate : 0.442 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: 0.7643 (m) cc_final: 0.7431 (m) REVERT: A 411 MET cc_start: 0.8525 (tmm) cc_final: 0.7998 (tmm) REVERT: A 453 CYS cc_start: 0.8829 (t) cc_final: 0.8465 (t) REVERT: L 107 SER cc_start: 0.9302 (m) cc_final: 0.8646 (p) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.3158 time to fit residues: 25.4184 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 : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 2 optimal weight: 0.2980 chunk 8 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.133776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.112284 restraints weight = 15442.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.116465 restraints weight = 7573.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.118922 restraints weight = 4689.890| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2780 Z= 0.195 Angle : 0.485 4.576 3774 Z= 0.265 Chirality : 0.034 0.120 427 Planarity : 0.003 0.026 440 Dihedral : 3.427 15.456 359 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.34 % Allowed : 1.69 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.81 (0.44), residues: 319 helix: 2.98 (0.29), residues: 264 sheet: None (None), residues: 0 loop : 0.04 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 202 HIS 0.003 0.001 HIS A 130 PHE 0.008 0.001 PHE A 110 TYR 0.016 0.001 TYR A 281 ARG 0.001 0.000 ARG A 39 *********************** 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 70 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 69 time to evaluate : 0.382 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 166 ILE cc_start: 0.8134 (pt) cc_final: 0.7893 (pt) REVERT: A 226 THR cc_start: 0.7656 (m) cc_final: 0.7437 (m) REVERT: A 409 HIS cc_start: 0.7951 (m-70) cc_final: 0.7700 (m-70) REVERT: A 411 MET cc_start: 0.8479 (tmm) cc_final: 0.8020 (tmm) REVERT: A 453 CYS cc_start: 0.8809 (t) cc_final: 0.8416 (t) REVERT: L 107 SER cc_start: 0.9336 (m) cc_final: 0.8626 (p) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.2900 time to fit residues: 24.4346 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 : 0.382 ------------------------------------------------------------------------------- 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: 0.9980 chunk 24 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 2 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 3 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.133798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.112515 restraints weight = 15369.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.116737 restraints weight = 7275.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.119066 restraints weight = 4385.678| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.3840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2780 Z= 0.184 Angle : 0.479 4.725 3774 Z= 0.261 Chirality : 0.034 0.118 427 Planarity : 0.003 0.026 440 Dihedral : 3.419 15.689 359 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.45), residues: 319 helix: 3.09 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.00 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 115 HIS 0.003 0.001 HIS A 409 PHE 0.006 0.001 PHE A 213 TYR 0.015 0.001 TYR A 281 ARG 0.003 0.000 ARG A 126 *********************** 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 72 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.385 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: 0.6981 (mm) cc_final: 0.6688 (mm) REVERT: A 166 ILE cc_start: 0.8098 (pt) cc_final: 0.7861 (pt) REVERT: A 226 THR cc_start: 0.7646 (m) cc_final: 0.7435 (m) REVERT: A 411 MET cc_start: 0.8456 (tmm) cc_final: 0.8069 (tmm) REVERT: A 453 CYS cc_start: 0.8832 (t) cc_final: 0.8428 (t) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.3097 time to fit residues: 26.5168 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 : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 29 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 11 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3846 r_free = 0.3846 target = 0.132828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111515 restraints weight = 15397.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115832 restraints weight = 7296.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118358 restraints weight = 4384.851| |-----------------------------------------------------------------------------| r_work (final): 0.3613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7165 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2780 Z= 0.183 Angle : 0.477 4.940 3774 Z= 0.261 Chirality : 0.034 0.117 427 Planarity : 0.003 0.026 440 Dihedral : 3.402 15.692 359 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 5.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.94 (0.45), residues: 319 helix: 3.08 (0.29), residues: 264 sheet: None (None), residues: 0 loop : 0.04 (0.84), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 115 HIS 0.003 0.001 HIS A 409 PHE 0.009 0.001 PHE L 102 TYR 0.014 0.001 TYR A 281 ARG 0.003 0.001 ARG A 126 *********************** 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 69 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.359 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 166 ILE cc_start: 0.8080 (pt) cc_final: 0.7860 (pt) REVERT: A 226 THR cc_start: 0.7613 (m) cc_final: 0.7410 (m) REVERT: A 453 CYS cc_start: 0.8836 (t) cc_final: 0.8433 (t) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.3105 time to fit residues: 25.4230 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 : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 21 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.0970 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.2980 chunk 24 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 HIS ** 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 = 0.3839 r_free = 0.3839 target = 0.132635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111222 restraints weight = 15506.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.115522 restraints weight = 7378.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.118061 restraints weight = 4444.571| |-----------------------------------------------------------------------------| r_work (final): 0.3611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.4130 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= 0.170 Angle : 0.474 5.100 3774 Z= 0.257 Chirality : 0.034 0.115 427 Planarity : 0.003 0.026 440 Dihedral : 3.373 15.506 359 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.45), residues: 319 helix: 3.11 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.02 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 115 HIS 0.002 0.001 HIS A 409 PHE 0.011 0.001 PHE A 112 TYR 0.013 0.001 TYR A 281 ARG 0.002 0.000 ARG A 126 *********************** 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 66 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.388 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: 0.8090 (pt) cc_final: 0.7864 (pt) REVERT: A 226 THR cc_start: 0.7585 (m) cc_final: 0.7368 (m) REVERT: A 411 MET cc_start: 0.8644 (tmm) cc_final: 0.8144 (tmm) REVERT: A 453 CYS cc_start: 0.8852 (t) cc_final: 0.8434 (t) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.3050 time to fit residues: 24.0510 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 : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 5 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 25 optimal weight: 6.9990 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 9 optimal weight: 0.0060 chunk 2 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 HIS ** 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 = 0.3847 r_free = 0.3847 target = 0.133338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.111640 restraints weight = 15466.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.115919 restraints weight = 7371.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.118558 restraints weight = 4475.717| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 2780 Z= 0.163 Angle : 0.468 5.559 3774 Z= 0.250 Chirality : 0.033 0.113 427 Planarity : 0.003 0.026 440 Dihedral : 3.370 15.471 359 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 5.16 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.04 (0.45), residues: 319 helix: 3.17 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.04 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 115 HIS 0.002 0.001 HIS A 409 PHE 0.010 0.001 PHE A 112 TYR 0.012 0.001 TYR A 281 ARG 0.001 0.000 ARG A 126 ********************** 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 70 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.347 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: 0.8078 (pt) cc_final: 0.7850 (pt) REVERT: A 226 THR cc_start: 0.7569 (m) cc_final: 0.7350 (m) REVERT: A 411 MET cc_start: 0.8550 (tmm) cc_final: 0.8015 (tmm) REVERT: A 453 CYS cc_start: 0.8666 (t) cc_final: 0.8257 (t) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.2913 time to fit residues: 24.6082 Evaluate side-chains 60 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 5 optimal weight: 2.9990 chunk 28 optimal weight: 0.0980 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 18 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 7 optimal weight: 0.8980 chunk 4 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 409 HIS ** 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 = 0.3853 r_free = 0.3853 target = 0.133592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.111518 restraints weight = 15453.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.115903 restraints weight = 7466.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.118415 restraints weight = 4507.140| |-----------------------------------------------------------------------------| r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2780 Z= 0.164 Angle : 0.461 5.170 3774 Z= 0.251 Chirality : 0.034 0.115 427 Planarity : 0.003 0.026 440 Dihedral : 3.384 15.879 359 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.34 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.97 (0.45), residues: 319 helix: 3.11 (0.29), residues: 264 sheet: None (None), residues: 0 loop : 0.01 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 115 HIS 0.002 0.001 HIS A 130 PHE 0.009 0.001 PHE A 112 TYR 0.013 0.001 TYR A 281 ARG 0.001 0.000 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2694.55 seconds wall clock time: 46 minutes 29.66 seconds (2789.66 seconds total)