Starting phenix.real_space_refine on Mon Sep 23 21:26:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/09_2024/7ru6_24698.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/09_2024/7ru6_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/09_2024/7ru6_24698.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/09_2024/7ru6_24698.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/09_2024/7ru6_24698.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru6_24698/09_2024/7ru6_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-5461/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: 3.33, per 1000 atoms: 0.61 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: 1.51 Conformation dependent library (CDL) restraints added in 452.6 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: 0.47 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: 1.76 Time building geometry restraints manager: 1.80 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: 0.340 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.780 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:2.970 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 fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.426 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: 0.3087 time to fit residues: 21.7513 Evaluate side-chains 56 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.431 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 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 fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.483 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 54 TYR cc_start: 0.8636 (t80) cc_final: 0.8425 (t80) REVERT: A 142 ILE cc_start: 0.7043 (mm) cc_final: 0.6707 (mm) REVERT: A 175 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: A 226 THR cc_start: 0.7639 (m) cc_final: 0.7431 (m) REVERT: A 411 MET cc_start: 0.8303 (tmm) cc_final: 0.7848 (tmm) outliers start: 1 outliers final: 0 residues processed: 72 average time/residue: 0.3426 time to fit residues: 29.2657 Evaluate side-chains 62 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 61 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 16 optimal weight: 0.9990 chunk 9 optimal weight: 0.0980 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 28 optimal weight: 0.5980 chunk 23 optimal weight: 0.4980 chunk 21 optimal weight: 0.8980 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 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6751 moved from start: 0.2928 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= 0.173 Angle : 0.478 4.951 3774 Z= 0.267 Chirality : 0.034 0.117 427 Planarity : 0.003 0.025 440 Dihedral : 3.462 14.927 359 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % 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: 3.65 (0.44), residues: 319 helix: 2.90 (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 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 fitting. rotamer outliers: 0 poor density : 68 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: A 188 GLU cc_start: 0.8716 (tt0) cc_final: 0.7851 (mt-10) REVERT: A 226 THR cc_start: 0.7606 (m) cc_final: 0.7404 (m) REVERT: A 411 MET cc_start: 0.8189 (tmm) cc_final: 0.7668 (tmm) REVERT: A 453 CYS cc_start: 0.9269 (t) cc_final: 0.9047 (t) REVERT: L 107 SER cc_start: 0.9017 (m) cc_final: 0.8192 (p) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2951 time to fit residues: 24.1306 Evaluate side-chains 57 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 17 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6812 moved from start: 0.3301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2780 Z= 0.248 Angle : 0.522 5.247 3774 Z= 0.294 Chirality : 0.035 0.129 427 Planarity : 0.003 0.024 440 Dihedral : 3.581 15.310 359 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % 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: 3.40 (0.43), residues: 319 helix: 2.71 (0.28), residues: 264 sheet: None (None), residues: 0 loop : -0.17 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 202 HIS 0.006 0.002 HIS A 130 PHE 0.010 0.001 PHE A 112 TYR 0.023 0.002 TYR A 225 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 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.457 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 188 GLU cc_start: 0.8734 (tt0) cc_final: 0.8151 (tm-30) REVERT: A 226 THR cc_start: 0.7732 (m) cc_final: 0.7500 (m) REVERT: A 271 GLN cc_start: 0.8555 (mt0) cc_final: 0.8281 (mt0) REVERT: A 411 MET cc_start: 0.8195 (tmm) cc_final: 0.7664 (tmm) REVERT: A 453 CYS cc_start: 0.9201 (t) cc_final: 0.8820 (t) REVERT: L 106 TYR cc_start: 0.9169 (m-80) cc_final: 0.8956 (m-80) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.2931 time to fit residues: 24.0911 Evaluate side-chains 53 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.0770 chunk 18 optimal weight: 1.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 moved from start: 0.3522 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= 0.188 Angle : 0.474 4.417 3774 Z= 0.263 Chirality : 0.034 0.116 427 Planarity : 0.003 0.026 440 Dihedral : 3.506 15.828 359 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 : 2.70 % Favored : 96.96 % 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: 3.65 (0.44), residues: 319 helix: 2.89 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.10 (0.83), 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 135 TYR 0.017 0.001 TYR A 281 ARG 0.001 0.000 ARG A 200 *********************** 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 fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.459 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 61 MET cc_start: 0.7754 (mmt) cc_final: 0.7537 (mmm) REVERT: A 226 THR cc_start: 0.7775 (m) cc_final: 0.7558 (m) REVERT: A 411 MET cc_start: 0.8217 (tmm) cc_final: 0.7670 (tmm) REVERT: A 453 CYS cc_start: 0.9160 (t) cc_final: 0.8910 (t) REVERT: L 106 TYR cc_start: 0.9161 (m-80) cc_final: 0.8918 (m-80) REVERT: L 107 SER cc_start: 0.9019 (m) cc_final: 0.8072 (p) REVERT: L 109 TYR cc_start: 0.8688 (p90) cc_final: 0.8117 (p90) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.3189 time to fit residues: 25.7843 Evaluate side-chains 54 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 54 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 7 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.0060 chunk 22 optimal weight: 0.0980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6793 moved from start: 0.3767 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= 0.175 Angle : 0.468 4.634 3774 Z= 0.256 Chirality : 0.034 0.116 427 Planarity : 0.003 0.026 440 Dihedral : 3.424 15.423 359 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: 2.99 (0.29), residues: 264 sheet: None (None), residues: 0 loop : 0.07 (0.84), 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 409 PHE 0.008 0.001 PHE A 110 TYR 0.016 0.001 TYR A 281 ARG 0.004 0.001 ARG A 126 *********************** 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 71 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.439 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 61 MET cc_start: 0.7751 (mmt) cc_final: 0.7501 (mmm) REVERT: A 166 ILE cc_start: 0.7819 (pt) cc_final: 0.7611 (pt) REVERT: A 226 THR cc_start: 0.7692 (m) cc_final: 0.7480 (m) REVERT: A 411 MET cc_start: 0.8189 (tmm) cc_final: 0.7654 (tmm) REVERT: A 453 CYS cc_start: 0.9113 (t) cc_final: 0.8829 (t) REVERT: L 106 TYR cc_start: 0.9177 (m-80) cc_final: 0.8933 (m-80) REVERT: L 107 SER cc_start: 0.9036 (m) cc_final: 0.8054 (p) REVERT: L 109 TYR cc_start: 0.8660 (p90) cc_final: 0.8031 (p90) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.3169 time to fit residues: 26.7417 Evaluate side-chains 57 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 17 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** A 409 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.3803 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= 0.212 Angle : 0.493 4.689 3774 Z= 0.275 Chirality : 0.034 0.124 427 Planarity : 0.003 0.025 440 Dihedral : 3.506 15.628 359 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.34 % Allowed : 0.68 % Favored : 98.99 % 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: 3.66 (0.44), residues: 319 helix: 2.89 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.06 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP L 115 HIS 0.003 0.001 HIS A 130 PHE 0.010 0.001 PHE A 112 TYR 0.016 0.001 TYR A 281 ARG 0.003 0.001 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 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.436 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 61 MET cc_start: 0.7676 (mmt) cc_final: 0.7441 (mmm) REVERT: A 142 ILE cc_start: 0.6953 (mm) cc_final: 0.6600 (mm) REVERT: A 166 ILE cc_start: 0.7792 (pt) cc_final: 0.7586 (pt) REVERT: A 226 THR cc_start: 0.7775 (m) cc_final: 0.7563 (m) REVERT: A 411 MET cc_start: 0.8153 (tmm) cc_final: 0.7709 (tmm) REVERT: A 453 CYS cc_start: 0.9087 (t) cc_final: 0.8807 (t) REVERT: L 106 TYR cc_start: 0.9196 (m-80) cc_final: 0.8964 (m-80) REVERT: L 107 SER cc_start: 0.9014 (m) cc_final: 0.8111 (p) REVERT: L 109 TYR cc_start: 0.8654 (p90) cc_final: 0.8442 (p90) outliers start: 1 outliers final: 0 residues processed: 68 average time/residue: 0.3076 time to fit residues: 24.9542 Evaluate side-chains 55 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.9980 chunk 2 optimal weight: 0.0170 chunk 24 optimal weight: 6.9990 chunk 28 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.5820 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6820 moved from start: 0.4142 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= 0.174 Angle : 0.491 6.667 3774 Z= 0.264 Chirality : 0.034 0.115 427 Planarity : 0.003 0.026 440 Dihedral : 3.414 15.523 359 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.34 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: 3.81 (0.45), residues: 319 helix: 2.99 (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 0.007 0.001 TRP A 284 HIS 0.002 0.001 HIS A 130 PHE 0.009 0.001 PHE A 112 TYR 0.015 0.001 TYR A 281 ARG 0.002 0.000 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 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.447 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 226 THR cc_start: 0.7753 (m) cc_final: 0.7538 (m) REVERT: A 411 MET cc_start: 0.8119 (tmm) cc_final: 0.7585 (tmm) REVERT: A 453 CYS cc_start: 0.9077 (t) cc_final: 0.8792 (t) REVERT: L 106 TYR cc_start: 0.9191 (m-80) cc_final: 0.8942 (m-80) REVERT: L 107 SER cc_start: 0.9017 (m) cc_final: 0.8040 (p) REVERT: L 109 TYR cc_start: 0.8693 (p90) cc_final: 0.8462 (p90) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3305 time to fit residues: 26.5584 Evaluate side-chains 57 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 27 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 19 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.4162 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 : 0.491 4.886 3774 Z= 0.270 Chirality : 0.034 0.121 427 Planarity : 0.003 0.025 440 Dihedral : 3.474 15.680 359 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: 3.76 (0.45), residues: 319 helix: 2.97 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.11 (0.85), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 115 HIS 0.003 0.001 HIS A 409 PHE 0.006 0.001 PHE A 213 TYR 0.014 0.002 TYR A 281 ARG 0.002 0.000 ARG A 39 *********************** 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 68 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 0.440 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: 0.7770 (m) cc_final: 0.7545 (m) REVERT: A 411 MET cc_start: 0.8073 (tmm) cc_final: 0.7536 (tmm) REVERT: A 453 CYS cc_start: 0.9062 (t) cc_final: 0.8771 (t) REVERT: L 106 TYR cc_start: 0.9203 (m-80) cc_final: 0.8961 (m-80) REVERT: L 107 SER cc_start: 0.9026 (m) cc_final: 0.8029 (p) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3057 time to fit residues: 24.8637 Evaluate side-chains 57 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 15 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 27 optimal weight: 0.1980 chunk 7 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2780 Z= 0.197 Angle : 0.526 7.214 3774 Z= 0.284 Chirality : 0.035 0.126 427 Planarity : 0.003 0.025 440 Dihedral : 3.551 15.924 359 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % 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: 3.50 (0.44), residues: 319 helix: 2.81 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.30 (0.83), residues: 55 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP L 115 HIS 0.007 0.002 HIS A 130 PHE 0.011 0.001 PHE A 110 TYR 0.015 0.002 TYR A 225 ARG 0.002 0.000 ARG A 39 ********************** 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 fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.456 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: 0.7668 (m) cc_final: 0.7464 (m) REVERT: A 411 MET cc_start: 0.8109 (tmm) cc_final: 0.7573 (tmm) REVERT: A 453 CYS cc_start: 0.9012 (t) cc_final: 0.8771 (t) REVERT: L 106 TYR cc_start: 0.9204 (m-80) cc_final: 0.8971 (m-80) REVERT: L 107 SER cc_start: 0.9028 (m) cc_final: 0.8047 (p) outliers start: 0 outliers final: 0 residues processed: 70 average time/residue: 0.3060 time to fit residues: 25.8106 Evaluate side-chains 56 residues out of total 296 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 56 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.1980 chunk 31 optimal weight: 0.6980 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 409 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.131882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110873 restraints weight = 15443.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.115030 restraints weight = 7420.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.117507 restraints weight = 4482.349| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.4490 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= 0.186 Angle : 0.500 5.447 3774 Z= 0.271 Chirality : 0.034 0.117 427 Planarity : 0.003 0.025 440 Dihedral : 3.554 16.052 359 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.00 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: 3.52 (0.44), residues: 319 helix: 2.85 (0.29), residues: 264 sheet: None (None), residues: 0 loop : -0.48 (0.81), 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 0.005 0.001 PHE A 135 TYR 0.016 0.001 TYR A 225 ARG 0.004 0.001 ARG A 126 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2273.66 seconds wall clock time: 39 minutes 59.24 seconds (2399.24 seconds total)