Starting phenix.real_space_refine on Fri Dec 27 06:38:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvl_34131/12_2024/7yvl_34131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvl_34131/12_2024/7yvl_34131.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvl_34131/12_2024/7yvl_34131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvl_34131/12_2024/7yvl_34131.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvl_34131/12_2024/7yvl_34131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvl_34131/12_2024/7yvl_34131.cif" } resolution = 3.3 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= -0.001 sd= 0.028 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: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 2066 2.51 5 N 531 2.21 5 O 613 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3224 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 917 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "C" Number of atoms: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 796 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "B" Number of atoms: 1511 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1511 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 4.92, per 1000 atoms: 1.53 Number of scatterers: 3224 At special positions: 0 Unit cell: (81.18, 71.34, 95.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 613 8.00 N 531 7.00 C 2066 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 97 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 90 " distance=2.04 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.02 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.05 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.12 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.93 Conformation dependent library (CDL) restraints added in 399.7 milliseconds 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 772 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 6.7% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 88 through 92 removed outlier: 3.801A pdb=" N THR A 92 " --> pdb=" O PRO A 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 85 removed outlier: 3.601A pdb=" N ASP C 85 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 349 through 353 removed outlier: 4.105A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 403 through 410 removed outlier: 3.843A pdb=" N GLU B 406 " --> pdb=" O ARG B 403 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N VAL B 407 " --> pdb=" O GLY B 404 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 506 removed outlier: 3.707A pdb=" N GLN B 506 " --> pdb=" O VAL B 503 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 3.605A pdb=" N THR A 83 " --> pdb=" O THR A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 61 removed outlier: 5.617A pdb=" N TRP A 49 " --> pdb=" O ARG A 40 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ARG A 40 " --> pdb=" O TRP A 49 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N ALA A 51 " --> pdb=" O TRP A 38 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N TYR A 95 " --> pdb=" O THR A 113 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR A 113 " --> pdb=" O TYR A 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 9 through 10 removed outlier: 6.990A pdb=" N TRP C 37 " --> pdb=" O MET C 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 9 through 10 removed outlier: 3.545A pdb=" N VAL C 99 " --> pdb=" O SER C 92 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 18 through 20 Processing sheet with id=AA7, first strand: chain 'B' and resid 357 through 358 removed outlier: 4.264A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 509 " --> pdb=" O TRP B 436 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL B 433 " --> pdb=" O LYS B 378 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LYS B 378 " --> pdb=" O VAL B 433 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 452 through 454 81 hydrogen bonds defined for protein. 174 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: 0.80 Time building geometry restraints manager: 0.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 506 1.28 - 1.42: 949 1.42 - 1.56: 1839 1.56 - 1.71: 0 1.71 - 1.85: 16 Bond restraints: 3310 Sorted by residual: bond pdb=" C TYR C 38 " pdb=" N GLN C 39 " ideal model delta sigma weight residual 1.331 1.533 -0.202 1.65e-02 3.67e+03 1.50e+02 bond pdb=" CA TYR C 93 " pdb=" C TYR C 93 " ideal model delta sigma weight residual 1.524 1.398 0.126 1.26e-02 6.30e+03 9.99e+01 bond pdb=" C ILE A 102 " pdb=" O ILE A 102 " ideal model delta sigma weight residual 1.242 1.161 0.081 8.60e-03 1.35e+04 8.86e+01 bond pdb=" C TYR C 93 " pdb=" O TYR C 93 " ideal model delta sigma weight residual 1.234 1.137 0.097 1.19e-02 7.06e+03 6.67e+01 bond pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta sigma weight residual 1.539 1.495 0.044 5.40e-03 3.43e+04 6.58e+01 ... (remaining 3305 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 4323 2.52 - 5.03: 163 5.03 - 7.55: 19 7.55 - 10.07: 4 10.07 - 12.59: 7 Bond angle restraints: 4516 Sorted by residual: angle pdb=" N ILE A 102 " pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta sigma weight residual 110.45 118.23 -7.78 7.80e-01 1.64e+00 9.95e+01 angle pdb=" O TYR C 38 " pdb=" C TYR C 38 " pdb=" N GLN C 39 " ideal model delta sigma weight residual 123.27 134.47 -11.20 1.22e+00 6.72e-01 8.43e+01 angle pdb=" C TYR C 93 " pdb=" CA TYR C 93 " pdb=" CB TYR C 93 " ideal model delta sigma weight residual 109.72 97.13 12.59 1.66e+00 3.63e-01 5.75e+01 angle pdb=" CA TYR C 38 " pdb=" C TYR C 38 " pdb=" N GLN C 39 " ideal model delta sigma weight residual 116.00 105.28 10.72 1.50e+00 4.44e-01 5.11e+01 angle pdb=" C SER C 97 " pdb=" CA SER C 97 " pdb=" CB SER C 97 " ideal model delta sigma weight residual 109.99 99.03 10.96 1.61e+00 3.86e-01 4.63e+01 ... (remaining 4511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 1708 15.10 - 30.20: 180 30.20 - 45.29: 45 45.29 - 60.39: 9 60.39 - 75.49: 2 Dihedral angle restraints: 1944 sinusoidal: 727 harmonic: 1217 Sorted by residual: dihedral pdb=" CB CYS B 480 " pdb=" SG CYS B 480 " pdb=" SG CYS B 488 " pdb=" CB CYS B 488 " ideal model delta sinusoidal sigma weight residual 93.00 168.49 -75.49 1 1.00e+01 1.00e-02 7.19e+01 dihedral pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta harmonic sigma weight residual 123.40 141.60 -18.20 0 2.50e+00 1.60e-01 5.30e+01 dihedral pdb=" C ILE A 102 " pdb=" N ILE A 102 " pdb=" CA ILE A 102 " pdb=" CB ILE A 102 " ideal model delta harmonic sigma weight residual -122.00 -139.22 17.22 0 2.50e+00 1.60e-01 4.74e+01 ... (remaining 1941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 487 0.159 - 0.317: 13 0.317 - 0.476: 2 0.476 - 0.635: 0 0.635 - 0.793: 1 Chirality restraints: 503 Sorted by residual: chirality pdb=" CA ILE A 102 " pdb=" N ILE A 102 " pdb=" C ILE A 102 " pdb=" CB ILE A 102 " both_signs ideal model delta sigma weight residual False 2.43 1.64 0.79 2.00e-01 2.50e+01 1.57e+01 chirality pdb=" CA SER C 96 " pdb=" N SER C 96 " pdb=" C SER C 96 " pdb=" CB SER C 96 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.44e+00 chirality pdb=" CA THR C 95 " pdb=" N THR C 95 " pdb=" C THR C 95 " pdb=" CB THR C 95 " both_signs ideal model delta sigma weight residual False 2.53 2.21 0.32 2.00e-01 2.50e+01 2.58e+00 ... (remaining 500 not shown) Planarity restraints: 574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 102 " -0.065 5.00e-02 4.00e+02 9.84e-02 1.55e+01 pdb=" N PRO A 103 " 0.170 5.00e-02 4.00e+02 pdb=" CA PRO A 103 " -0.052 5.00e-02 4.00e+02 pdb=" CD PRO A 103 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 485 " -0.018 2.00e-02 2.50e+03 3.55e-02 1.26e+01 pdb=" C GLY B 485 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY B 485 " -0.023 2.00e-02 2.50e+03 pdb=" N VAL B 486 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER C 97 " 0.013 2.00e-02 2.50e+03 2.71e-02 7.33e+00 pdb=" C SER C 97 " -0.047 2.00e-02 2.50e+03 pdb=" O SER C 97 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL C 98 " 0.016 2.00e-02 2.50e+03 ... (remaining 571 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.70: 183 2.70 - 3.25: 3086 3.25 - 3.80: 4704 3.80 - 4.35: 6139 4.35 - 4.90: 10672 Nonbonded interactions: 24784 Sorted by model distance: nonbonded pdb=" O ASN B 388 " pdb=" OD1 ASN B 388 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASP B 364 " pdb=" OG SER B 366 " model vdw 2.199 3.040 nonbonded pdb=" O SER A 119 " pdb=" OG SER A 119 " model vdw 2.251 3.040 nonbonded pdb=" O ILE A 105 " pdb=" OH TYR C 38 " model vdw 2.307 3.040 nonbonded pdb=" O THR A 92 " pdb=" OG1 THR A 92 " model vdw 2.366 3.040 ... (remaining 24779 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.050 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.240 Process input model: 14.760 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:3.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 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 : 0.011 0.202 3310 Z= 0.661 Angle : 1.163 12.585 4516 Z= 0.730 Chirality : 0.075 0.793 503 Planarity : 0.007 0.098 574 Dihedral : 12.977 71.126 1154 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 18.66 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.96 % Favored : 90.56 % Rotamer: Outliers : 1.42 % Allowed : 15.95 % Favored : 82.62 % Cbeta Deviations : 1.30 % 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: -4.93 (0.33), residues: 413 helix: -4.88 (0.35), residues: 29 sheet: -2.71 (0.37), residues: 143 loop : -3.55 (0.32), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP A 55 HIS 0.008 0.002 HIS A 99 PHE 0.016 0.002 PHE A 106 TYR 0.020 0.002 TYR B 489 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.370 Fit side-chains REVERT: A 17 THR cc_start: 0.7589 (m) cc_final: 0.7375 (m) REVERT: C 53 VAL cc_start: 0.8166 (t) cc_final: 0.7946 (t) REVERT: B 467 ASP cc_start: 0.7467 (p0) cc_final: 0.7161 (p0) outliers start: 5 outliers final: 1 residues processed: 121 average time/residue: 0.2000 time to fit residues: 28.2607 Evaluate side-chains 78 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 11 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: C 6 GLN B 505 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3310 Z= 0.236 Angle : 0.726 13.781 4516 Z= 0.356 Chirality : 0.046 0.183 503 Planarity : 0.005 0.030 574 Dihedral : 5.235 44.329 462 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.54 % Favored : 93.22 % Rotamer: Outliers : 4.84 % Allowed : 21.37 % Favored : 73.79 % 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: -3.62 (0.36), residues: 413 helix: -4.73 (0.46), residues: 22 sheet: -1.68 (0.40), residues: 145 loop : -2.74 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 55 HIS 0.001 0.001 HIS B 519 PHE 0.008 0.001 PHE B 347 TYR 0.019 0.001 TYR C 93 ARG 0.003 0.001 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.7944 (OUTLIER) cc_final: 0.7700 (mmtm) REVERT: C 62 ASN cc_start: 0.7016 (t0) cc_final: 0.6745 (t0) REVERT: B 357 ARG cc_start: 0.7591 (ttm170) cc_final: 0.6533 (mtt180) REVERT: B 467 ASP cc_start: 0.7544 (p0) cc_final: 0.7062 (p0) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.1562 time to fit residues: 18.4757 Evaluate side-chains 81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 45 LYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.0870 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.4980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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: 0.7867 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3310 Z= 0.262 Angle : 0.663 9.903 4516 Z= 0.341 Chirality : 0.045 0.161 503 Planarity : 0.004 0.034 574 Dihedral : 4.718 23.715 460 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.54 % Favored : 93.22 % Rotamer: Outliers : 6.27 % Allowed : 20.80 % Favored : 72.93 % 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: -3.09 (0.36), residues: 413 helix: -4.91 (0.31), residues: 20 sheet: -0.95 (0.42), residues: 136 loop : -2.57 (0.33), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 109 HIS 0.003 0.001 HIS A 99 PHE 0.008 0.002 PHE B 400 TYR 0.011 0.001 TYR C 93 ARG 0.004 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 73 time to evaluate : 0.365 Fit side-chains revert: symmetry clash REVERT: C 55 LYS cc_start: 0.7944 (ttmm) cc_final: 0.7725 (ttmm) REVERT: C 62 ASN cc_start: 0.7288 (t0) cc_final: 0.7001 (t0) REVERT: B 357 ARG cc_start: 0.7717 (ttm170) cc_final: 0.6467 (mtt180) REVERT: B 467 ASP cc_start: 0.7535 (p0) cc_final: 0.7246 (p0) outliers start: 22 outliers final: 15 residues processed: 90 average time/residue: 0.1568 time to fit residues: 17.0364 Evaluate side-chains 88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.6980 chunk 36 optimal weight: 0.3980 chunk 38 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7857 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3310 Z= 0.199 Angle : 0.618 8.772 4516 Z= 0.314 Chirality : 0.044 0.144 503 Planarity : 0.004 0.032 574 Dihedral : 4.677 24.963 460 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.26 % Favored : 92.49 % Rotamer: Outliers : 6.55 % Allowed : 23.08 % Favored : 70.37 % 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: -2.82 (0.36), residues: 413 helix: -4.91 (0.25), residues: 21 sheet: -0.55 (0.41), residues: 141 loop : -2.51 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.002 0.001 HIS B 519 PHE 0.008 0.001 PHE B 400 TYR 0.013 0.001 TYR C 93 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: C 55 LYS cc_start: 0.7999 (ttmm) cc_final: 0.7767 (ttmm) REVERT: C 62 ASN cc_start: 0.7373 (t0) cc_final: 0.7072 (t0) REVERT: B 357 ARG cc_start: 0.7715 (ttm170) cc_final: 0.6300 (mtt180) outliers start: 23 outliers final: 18 residues processed: 94 average time/residue: 0.1555 time to fit residues: 17.7240 Evaluate side-chains 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 58 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 370 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.5116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 3310 Z= 0.373 Angle : 0.715 8.070 4516 Z= 0.373 Chirality : 0.047 0.177 503 Planarity : 0.005 0.036 574 Dihedral : 5.399 24.628 460 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.96 % Favored : 90.80 % Rotamer: Outliers : 7.69 % Allowed : 23.08 % Favored : 69.23 % 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: -2.67 (0.37), residues: 413 helix: -5.07 (0.20), residues: 21 sheet: -0.48 (0.43), residues: 140 loop : -2.35 (0.34), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 49 HIS 0.003 0.002 HIS B 519 PHE 0.011 0.002 PHE B 375 TYR 0.014 0.002 TYR B 365 ARG 0.003 0.001 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 77 time to evaluate : 0.314 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 62 ASN cc_start: 0.7604 (t0) cc_final: 0.7240 (t0) REVERT: B 357 ARG cc_start: 0.7957 (ttm170) cc_final: 0.6427 (mtt180) outliers start: 27 outliers final: 21 residues processed: 98 average time/residue: 0.1465 time to fit residues: 17.6484 Evaluate side-chains 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7930 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 3310 Z= 0.214 Angle : 0.650 9.107 4516 Z= 0.329 Chirality : 0.045 0.167 503 Planarity : 0.004 0.033 574 Dihedral : 4.932 26.117 460 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.02 % Favored : 92.74 % Rotamer: Outliers : 7.69 % Allowed : 21.94 % Favored : 70.37 % 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: -2.47 (0.38), residues: 413 helix: -5.05 (0.21), residues: 21 sheet: -0.22 (0.44), residues: 139 loop : -2.29 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.002 0.001 HIS A 99 PHE 0.010 0.001 PHE B 342 TYR 0.013 0.001 TYR C 93 ARG 0.002 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 78 time to evaluate : 0.364 Fit side-chains REVERT: A 79 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8148 (mp) REVERT: C 62 ASN cc_start: 0.7555 (t0) cc_final: 0.7236 (t0) REVERT: B 357 ARG cc_start: 0.7870 (ttt180) cc_final: 0.6353 (mtt180) outliers start: 27 outliers final: 24 residues processed: 97 average time/residue: 0.1614 time to fit residues: 18.9397 Evaluate side-chains 100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 LEU Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.2980 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7932 moved from start: 0.5357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3310 Z= 0.211 Angle : 0.657 11.317 4516 Z= 0.328 Chirality : 0.045 0.196 503 Planarity : 0.004 0.051 574 Dihedral : 4.850 23.948 460 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.51 % Favored : 92.25 % Rotamer: Outliers : 7.41 % Allowed : 26.21 % Favored : 66.38 % 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: -2.36 (0.38), residues: 413 helix: -5.05 (0.21), residues: 21 sheet: -0.10 (0.44), residues: 139 loop : -2.23 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.002 0.001 HIS A 99 PHE 0.010 0.001 PHE B 342 TYR 0.012 0.001 TYR C 93 ARG 0.002 0.000 ARG C 63 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 78 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: C 62 ASN cc_start: 0.7569 (t0) cc_final: 0.7272 (t0) REVERT: B 357 ARG cc_start: 0.7863 (ttt180) cc_final: 0.6336 (mtt180) outliers start: 26 outliers final: 25 residues processed: 98 average time/residue: 0.1612 time to fit residues: 19.0704 Evaluate side-chains 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 76 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain C residue 83 GLU Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 386 LYS Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.4980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.0270 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.1980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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: 0.7892 moved from start: 0.5496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3310 Z= 0.159 Angle : 0.637 10.460 4516 Z= 0.314 Chirality : 0.045 0.185 503 Planarity : 0.004 0.051 574 Dihedral : 4.544 21.302 460 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.02 % Favored : 92.74 % Rotamer: Outliers : 8.26 % Allowed : 24.79 % Favored : 66.95 % 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: -2.18 (0.38), residues: 413 helix: -5.02 (0.22), residues: 21 sheet: 0.02 (0.44), residues: 139 loop : -2.10 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.001 0.000 HIS A 99 PHE 0.009 0.001 PHE B 342 TYR 0.012 0.001 TYR C 93 ARG 0.001 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 82 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: C 62 ASN cc_start: 0.7557 (t0) cc_final: 0.7295 (t0) REVERT: B 357 ARG cc_start: 0.7828 (ttt180) cc_final: 0.6320 (mtt180) outliers start: 29 outliers final: 24 residues processed: 104 average time/residue: 0.1639 time to fit residues: 20.4128 Evaluate side-chains 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.0770 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3310 Z= 0.189 Angle : 0.691 15.581 4516 Z= 0.330 Chirality : 0.045 0.177 503 Planarity : 0.004 0.046 574 Dihedral : 4.593 20.609 460 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.75 % Favored : 92.01 % Rotamer: Outliers : 7.98 % Allowed : 26.21 % Favored : 65.81 % 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: -2.11 (0.38), residues: 413 helix: -4.48 (0.43), residues: 27 sheet: 0.12 (0.44), residues: 139 loop : -2.04 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.001 0.000 HIS B 519 PHE 0.009 0.001 PHE B 342 TYR 0.009 0.001 TYR C 93 ARG 0.001 0.000 ARG B 403 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 75 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 41 GLN cc_start: 0.8762 (OUTLIER) cc_final: 0.8550 (tt0) REVERT: C 62 ASN cc_start: 0.7617 (t0) cc_final: 0.7351 (t0) REVERT: B 357 ARG cc_start: 0.7847 (ttt180) cc_final: 0.6300 (mtt180) outliers start: 28 outliers final: 24 residues processed: 96 average time/residue: 0.1671 time to fit residues: 19.2795 Evaluate side-chains 99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 74 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain C residue 27 SER Chi-restraints excluded: chain C residue 32 TYR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 1 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 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3310 Z= 0.213 Angle : 0.661 10.250 4516 Z= 0.329 Chirality : 0.045 0.173 503 Planarity : 0.004 0.049 574 Dihedral : 4.666 20.561 460 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.72 % Favored : 91.04 % Rotamer: Outliers : 6.84 % Allowed : 27.07 % Favored : 66.10 % 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: -2.02 (0.39), residues: 413 helix: -4.48 (0.43), residues: 27 sheet: 0.19 (0.45), residues: 139 loop : -1.99 (0.35), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 353 HIS 0.001 0.000 HIS B 519 PHE 0.010 0.001 PHE B 342 TYR 0.010 0.001 TYR C 93 ARG 0.002 0.000 ARG A 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.384 Fit side-chains REVERT: C 62 ASN cc_start: 0.7632 (t0) cc_final: 0.7360 (t0) REVERT: B 357 ARG cc_start: 0.7857 (ttt180) cc_final: 0.6293 (mtt180) outliers start: 24 outliers final: 22 residues processed: 95 average time/residue: 0.1548 time to fit residues: 17.8964 Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 69 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 18 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 385 THR Chi-restraints excluded: chain B residue 392 PHE Chi-restraints excluded: chain B residue 410 ILE Chi-restraints excluded: chain B residue 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 441 LEU Chi-restraints excluded: chain B residue 444 LYS Chi-restraints excluded: chain B residue 472 ILE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain B residue 511 VAL Chi-restraints excluded: chain B residue 524 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 36 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.116030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.102837 restraints weight = 6485.460| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.54 r_work: 0.3322 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.5858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3310 Z= 0.227 Angle : 0.692 10.103 4516 Z= 0.342 Chirality : 0.046 0.168 503 Planarity : 0.004 0.046 574 Dihedral : 4.824 20.704 460 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.96 % Favored : 90.80 % Rotamer: Outliers : 7.12 % Allowed : 26.78 % Favored : 66.10 % 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: -2.03 (0.39), residues: 413 helix: -4.48 (0.42), residues: 27 sheet: 0.22 (0.44), residues: 138 loop : -2.01 (0.36), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 353 HIS 0.001 0.001 HIS A 99 PHE 0.010 0.001 PHE A 24 TYR 0.010 0.001 TYR C 93 ARG 0.002 0.000 ARG A 68 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1589.60 seconds wall clock time: 29 minutes 37.50 seconds (1777.50 seconds total)