Starting phenix.real_space_refine on Tue Feb 11 11:25:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ru6_24698/02_2025/7ru6_24698.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ru6_24698/02_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_24698/02_2025/7ru6_24698.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ru6_24698/02_2025/7ru6_24698.map" model { file = "/net/cci-nas-00/data/ceres_data/7ru6_24698/02_2025/7ru6_24698.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ru6_24698/02_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-5592/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: 3.08, per 1000 atoms: 0.57 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: 1.57 Conformation dependent library (CDL) restraints added in 368.3 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: 0.34 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: 2.06 Time building geometry restraints manager: 1.88 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: 0.700 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: 16.690 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.540 ------------------------------------------------------------------------------- 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 : 0.563 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: 0.3097 time to fit residues: 21.8840 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 : 0.458 ------------------------------------------------------------------------------- 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 = 40)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114805 restraints weight = 14843.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.119189 restraints weight = 7374.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.121831 restraints weight = 4637.039| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- 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 : 0.433 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: 0.8527 (tm-30) REVERT: A 226 THR cc_start: 0.7547 (m) cc_final: 0.7328 (m) REVERT: A 411 MET cc_start: 0.8632 (tmm) cc_final: 0.8157 (tmm) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.3231 time to fit residues: 27.3847 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 : 0.399 ------------------------------------------------------------------------------- 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: 0.9980 chunk 9 optimal weight: 0.0980 chunk 12 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 14 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.136535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.114394 restraints weight = 15193.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.118637 restraints weight = 7386.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120985 restraints weight = 4565.169| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.2925 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= 0.174 Angle : 0.470 4.893 3774 Z= 0.262 Chirality : 0.033 0.116 427 Planarity : 0.003 0.025 440 Dihedral : 3.453 14.915 359 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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 (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: 3.70 (0.44), residues: 319 helix: 2.94 (0.29), residues: 262 sheet: None (None), residues: 0 loop : -0.05 (0.84), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 108 HIS 0.007 0.001 HIS A 130 PHE 0.012 0.001 PHE A 112 TYR 0.019 0.002 TYR A 281 ARG 0.001 0.000 ARG A 200 *********************** 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 : 0.414 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: 0.8717 (tt0) cc_final: 0.8185 (mt-10) REVERT: A 411 MET cc_start: 0.8554 (tmm) cc_final: 0.8006 (tmm) REVERT: A 453 CYS cc_start: 0.9021 (t) cc_final: 0.8758 (t) REVERT: L 107 SER cc_start: 0.9316 (m) cc_final: 0.8687 (p) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2961 time to fit residues: 24.2959 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 : 0.446 ------------------------------------------------------------------------------- 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: 0.9980 chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 22 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.134135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.111717 restraints weight = 15661.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.116093 restraints weight = 7568.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118678 restraints weight = 4631.043| |-----------------------------------------------------------------------------| r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.3285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2780 Z= 0.225 Angle : 0.503 5.155 3774 Z= 0.283 Chirality : 0.035 0.126 427 Planarity : 0.003 0.024 440 Dihedral : 3.533 15.370 359 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 0.34 % Allowed : 2.36 % Favored : 97.30 % 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: 3.61 (0.43), residues: 319 helix: 2.84 (0.28), residues: 264 sheet: None (None), residues: 0 loop : 0.01 (0.84), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 202 HIS 0.006 0.002 HIS A 130 PHE 0.010 0.001 PHE A 112 TYR 0.020 0.002 TYR A 281 ARG 0.002 0.000 ARG A 39 *********************** 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 : 0.427 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: A 166 ILE cc_start: 0.8072 (pt) cc_final: 0.7855 (pt) REVERT: A 188 GLU cc_start: 0.8716 (tt0) cc_final: 0.8384 (tm-30) REVERT: A 226 THR cc_start: 0.7692 (m) cc_final: 0.7434 (m) REVERT: A 411 MET cc_start: 0.8541 (tmm) cc_final: 0.8019 (tmm) REVERT: A 453 CYS cc_start: 0.9002 (t) cc_final: 0.8586 (t) outliers start: 1 outliers final: 0 residues processed: 67 average time/residue: 0.2985 time to fit residues: 24.2075 Evaluate side-chains 53 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.384 ------------------------------------------------------------------------------- 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: 0.7980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.4980 chunk 31 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3863 r_free = 0.3863 target = 0.133756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.112586 restraints weight = 15442.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.116882 restraints weight = 7383.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.119314 restraints weight = 4466.512| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.3502 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= 0.195 Angle : 0.482 4.503 3774 Z= 0.266 Chirality : 0.034 0.118 427 Planarity : 0.003 0.025 440 Dihedral : 3.504 15.711 359 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.98 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: 3.68 (0.44), residues: 319 helix: 2.92 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.16 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 190 HIS 0.004 0.001 HIS A 130 PHE 0.005 0.001 PHE A 344 TYR 0.017 0.001 TYR A 281 ARG 0.001 0.000 ARG A 100 *********************** 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 : 0.394 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: A 166 ILE cc_start: 0.8114 (pt) cc_final: 0.7914 (pt) REVERT: A 226 THR cc_start: 0.7667 (m) cc_final: 0.7441 (m) REVERT: A 409 HIS cc_start: 0.7956 (m-70) cc_final: 0.7738 (m-70) REVERT: A 411 MET cc_start: 0.8518 (tmm) cc_final: 0.8010 (tmm) REVERT: A 453 CYS cc_start: 0.8901 (t) cc_final: 0.8569 (t) REVERT: L 107 SER cc_start: 0.9343 (m) cc_final: 0.8485 (p) REVERT: L 109 TYR cc_start: 0.8985 (p90) cc_final: 0.8557 (p90) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.3260 time to fit residues: 26.5478 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 : 0.424 ------------------------------------------------------------------------------- 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: 0.7980 chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 0.0570 chunk 8 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 overall best weight: 0.7298 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.132744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.111806 restraints weight = 15568.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.116075 restraints weight = 7486.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.118574 restraints weight = 4539.454| |-----------------------------------------------------------------------------| r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3742 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= 0.204 Angle : 0.492 4.521 3774 Z= 0.269 Chirality : 0.034 0.119 427 Planarity : 0.003 0.026 440 Dihedral : 3.484 15.410 359 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 3.70 (0.44), residues: 319 helix: 2.91 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.01 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 202 HIS 0.004 0.001 HIS A 409 PHE 0.009 0.001 PHE A 110 TYR 0.017 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 : 0.431 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: 0.8104 (pt) cc_final: 0.7888 (pt) REVERT: A 226 THR cc_start: 0.7666 (m) cc_final: 0.7458 (m) REVERT: A 411 MET cc_start: 0.8473 (tmm) cc_final: 0.8020 (tmm) REVERT: A 453 CYS cc_start: 0.8813 (t) cc_final: 0.8396 (t) REVERT: L 107 SER cc_start: 0.9337 (m) cc_final: 0.8623 (p) outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 0.3060 time to fit residues: 25.6631 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 : 0.432 ------------------------------------------------------------------------------- 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: 0.5980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.2980 chunk 3 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3849 r_free = 0.3849 target = 0.133274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.111747 restraints weight = 15257.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.116116 restraints weight = 7278.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.118747 restraints weight = 4361.231| |-----------------------------------------------------------------------------| r_work (final): 0.3623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.3938 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= 0.182 Angle : 0.485 4.751 3774 Z= 0.263 Chirality : 0.034 0.115 427 Planarity : 0.003 0.026 440 Dihedral : 3.441 15.669 359 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.16 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: 3.85 (0.44), residues: 319 helix: 3.04 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.11 (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 0.006 0.001 PHE L 102 TYR 0.016 0.001 TYR A 281 ARG 0.002 0.001 ARG L 117 *********************** 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 70 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 0.435 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: 0.6979 (mm) cc_final: 0.6708 (mm) REVERT: A 166 ILE cc_start: 0.8101 (pt) cc_final: 0.7896 (pt) REVERT: A 226 THR cc_start: 0.7640 (m) cc_final: 0.7414 (m) REVERT: A 411 MET cc_start: 0.8459 (tmm) cc_final: 0.8023 (tmm) REVERT: A 453 CYS cc_start: 0.8766 (t) cc_final: 0.8386 (t) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3217 time to fit residues: 26.6991 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 31 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 28 optimal weight: 0.1980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.3861 r_free = 0.3861 target = 0.134289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.113081 restraints weight = 15209.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.117461 restraints weight = 7358.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.119977 restraints weight = 4449.791| |-----------------------------------------------------------------------------| r_work (final): 0.3646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.4076 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= 0.147 Angle : 0.448 5.177 3774 Z= 0.243 Chirality : 0.033 0.110 427 Planarity : 0.003 0.027 440 Dihedral : 3.359 15.570 359 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 4.42 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: 4.10 (0.45), residues: 319 helix: 3.21 (0.29), residues: 264 sheet: None (None), residues: 0 loop : 0.00 (0.81), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 190 HIS 0.002 0.001 HIS A 409 PHE 0.010 0.001 PHE A 209 TYR 0.012 0.001 TYR A 281 ARG 0.001 0.000 ARG A 200 *********************** 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 68 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.393 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 142 ILE cc_start: 0.6963 (mm) cc_final: 0.6716 (mm) REVERT: A 166 ILE cc_start: 0.8092 (pt) cc_final: 0.7885 (pt) REVERT: A 226 THR cc_start: 0.7562 (m) cc_final: 0.7354 (m) REVERT: A 411 MET cc_start: 0.8420 (tmm) cc_final: 0.8003 (tmm) REVERT: A 453 CYS cc_start: 0.8742 (t) cc_final: 0.8288 (t) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3009 time to fit residues: 24.5784 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 : 0.435 ------------------------------------------------------------------------------- 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: 0.9990 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 16 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 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 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.131709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.110328 restraints weight = 15519.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.114656 restraints weight = 7353.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.117262 restraints weight = 4411.343| |-----------------------------------------------------------------------------| r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.4233 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= 0.205 Angle : 0.497 4.978 3774 Z= 0.276 Chirality : 0.034 0.124 427 Planarity : 0.003 0.025 440 Dihedral : 3.475 15.899 359 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.27 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: 3.67 (0.44), residues: 319 helix: 2.92 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.22 (0.82), 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 130 PHE 0.009 0.001 PHE A 110 TYR 0.014 0.001 TYR A 281 ARG 0.002 0.001 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 64 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.393 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 170 LEU cc_start: 0.8480 (mm) cc_final: 0.8038 (tt) REVERT: A 226 THR cc_start: 0.7703 (m) cc_final: 0.7490 (m) REVERT: A 411 MET cc_start: 0.8424 (tmm) cc_final: 0.7988 (tmm) REVERT: A 453 CYS cc_start: 0.8877 (t) cc_final: 0.8495 (t) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.3110 time to fit residues: 23.8302 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 : 0.414 ------------------------------------------------------------------------------- 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: 1.9990 chunk 19 optimal weight: 0.5980 chunk 25 optimal weight: 0.0010 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 0.0870 chunk 13 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.4564 ------------------------------------------------------------------------------- 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 = 0.3851 r_free = 0.3851 target = 0.133685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.112273 restraints weight = 15404.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.116555 restraints weight = 7249.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.119083 restraints weight = 4361.078| |-----------------------------------------------------------------------------| r_work (final): 0.3622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.4273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2780 Z= 0.156 Angle : 0.468 5.182 3774 Z= 0.252 Chirality : 0.034 0.111 427 Planarity : 0.003 0.026 440 Dihedral : 3.468 15.820 359 Min Nonbonded Distance : 2.503 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 (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 (0.45), residues: 319 helix: 3.03 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.15 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 115 HIS 0.006 0.001 HIS A 130 PHE 0.004 0.001 PHE A 213 TYR 0.012 0.001 TYR A 281 ARG 0.001 0.000 ARG A 200 ********************** 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 68 residues out of total 296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.428 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: symmetry clash REVERT: A 226 THR cc_start: 0.7565 (m) cc_final: 0.7355 (m) REVERT: A 411 MET cc_start: 0.8416 (tmm) cc_final: 0.7938 (tmm) REVERT: A 453 CYS cc_start: 0.8841 (t) cc_final: 0.8436 (t) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3095 time to fit residues: 25.3794 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 : 0.440 ------------------------------------------------------------------------------- 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: 0.9990 chunk 2 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3822 r_free = 0.3822 target = 0.131577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.110062 restraints weight = 15544.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.114271 restraints weight = 7407.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.116849 restraints weight = 4511.745| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.4391 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= 0.200 Angle : 0.502 4.982 3774 Z= 0.277 Chirality : 0.034 0.122 427 Planarity : 0.003 0.025 440 Dihedral : 3.530 16.043 359 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.56 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: 3.53 (0.44), residues: 319 helix: 2.84 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.35 (0.82), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP L 115 HIS 0.010 0.002 HIS A 130 PHE 0.008 0.001 PHE A 110 TYR 0.013 0.001 TYR A 281 ARG 0.002 0.001 ARG A 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2693.55 seconds wall clock time: 48 minutes 6.82 seconds (2886.82 seconds total)