Starting phenix.real_space_refine on Wed Mar 5 18:12:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvl_34131/03_2025/7yvl_34131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvl_34131/03_2025/7yvl_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_34131/03_2025/7yvl_34131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvl_34131/03_2025/7yvl_34131.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvl_34131/03_2025/7yvl_34131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvl_34131/03_2025/7yvl_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-5624/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: 5.35, per 1000 atoms: 1.66 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: 0.67 Conformation dependent library (CDL) restraints added in 367.1 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: 0.42 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: 0.90 Time building geometry restraints manager: 0.83 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: 9.700 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.800 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: 0.000 Load rotamer database and sin/cos tables:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.740 ------------------------------------------------------------------------------- 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 : 0.348 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: 0.1949 time to fit residues: 27.4983 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 : 0.332 ------------------------------------------------------------------------------- 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: 0.7980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 36 optimal weight: 0.1980 chunk 11 optimal weight: 0.7980 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.126404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.109976 restraints weight = 6378.767| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 2.88 r_work: 0.3414 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 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 13.778 4516 Z= 0.356 Chirality : 0.046 0.183 503 Planarity : 0.005 0.030 574 Dihedral : 5.235 44.328 462 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 : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 45 LYS cc_start: 0.8228 (OUTLIER) cc_final: 0.7941 (mmtm) REVERT: A 59 LYS cc_start: 0.8370 (mtmt) cc_final: 0.8029 (mttm) REVERT: C 62 ASN cc_start: 0.7228 (t0) cc_final: 0.6959 (t0) REVERT: B 357 ARG cc_start: 0.7850 (ttm170) cc_final: 0.6539 (mtt180) REVERT: B 467 ASP cc_start: 0.7764 (p0) cc_final: 0.7167 (p0) outliers start: 17 outliers final: 10 residues processed: 99 average time/residue: 0.1811 time to fit residues: 22.0192 Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 71 time to evaluate : 0.349 ------------------------------------------------------------------------------- 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 11 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 29 optimal weight: 0.0970 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 0.1980 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.123537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.107723 restraints weight = 6357.576| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.84 r_work: 0.3382 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 3310 Z= 0.201 Angle : 0.628 10.674 4516 Z= 0.319 Chirality : 0.045 0.150 503 Planarity : 0.004 0.030 574 Dihedral : 4.439 23.495 460 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.05 % Favored : 93.70 % Rotamer: Outliers : 5.13 % Allowed : 21.65 % Favored : 73.22 % 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: -3.01 (0.36), residues: 413 helix: -4.75 (0.44), residues: 20 sheet: -0.89 (0.42), residues: 136 loop : -2.52 (0.33), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 109 HIS 0.002 0.001 HIS A 99 PHE 0.008 0.001 PHE B 400 TYR 0.012 0.001 TYR A 108 ARG 0.003 0.000 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 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 59 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8311 (mttm) REVERT: C 62 ASN cc_start: 0.7373 (t0) cc_final: 0.7103 (t0) REVERT: B 357 ARG cc_start: 0.7935 (ttm170) cc_final: 0.6505 (mtt180) REVERT: B 362 VAL cc_start: 0.6277 (t) cc_final: 0.5999 (p) REVERT: B 467 ASP cc_start: 0.7706 (p0) cc_final: 0.7084 (p0) outliers start: 18 outliers final: 12 residues processed: 89 average time/residue: 0.1619 time to fit residues: 17.2760 Evaluate side-chains 85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 0.359 ------------------------------------------------------------------------------- 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 115 VAL Chi-restraints excluded: chain C residue 11 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 433 VAL Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 444 LYS 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 35 optimal weight: 0.0980 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.2980 chunk 26 optimal weight: 0.5980 overall best weight: 0.5382 ------------------------------------------------------------------------------- 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 = 0.3689 r_free = 0.3689 target = 0.122167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.106489 restraints weight = 6513.982| |-----------------------------------------------------------------------------| r_work (start): 0.3463 rms_B_bonded: 2.81 r_work: 0.3377 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3310 Z= 0.186 Angle : 0.610 8.673 4516 Z= 0.307 Chirality : 0.044 0.141 503 Planarity : 0.004 0.032 574 Dihedral : 4.498 24.714 460 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.02 % Favored : 92.74 % Rotamer: Outliers : 7.12 % Allowed : 22.51 % 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: -2.65 (0.37), residues: 413 helix: -4.78 (0.35), residues: 21 sheet: -0.34 (0.43), residues: 135 loop : -2.43 (0.33), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 49 HIS 0.002 0.001 HIS A 99 PHE 0.008 0.001 PHE B 400 TYR 0.012 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 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 79 time to evaluate : 0.362 Fit side-chains REVERT: A 35 SER cc_start: 0.8645 (p) cc_final: 0.8431 (t) REVERT: C 62 ASN cc_start: 0.7490 (t0) cc_final: 0.7206 (t0) REVERT: B 357 ARG cc_start: 0.7906 (ttm170) cc_final: 0.6367 (mtt180) REVERT: B 362 VAL cc_start: 0.6471 (t) cc_final: 0.6258 (p) REVERT: B 467 ASP cc_start: 0.7700 (p0) cc_final: 0.7405 (p0) outliers start: 25 outliers final: 19 residues processed: 96 average time/residue: 0.1553 time to fit residues: 18.0078 Evaluate side-chains 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.357 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain A residue 115 VAL 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 C residue 95 THR Chi-restraints excluded: chain B residue 382 VAL 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 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 30 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 28 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.118794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.104546 restraints weight = 6480.975| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.65 r_work: 0.3351 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8071 moved from start: 0.4712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3310 Z= 0.220 Angle : 0.616 8.391 4516 Z= 0.316 Chirality : 0.044 0.134 503 Planarity : 0.004 0.032 574 Dihedral : 4.619 22.653 460 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.75 % Favored : 92.01 % Rotamer: Outliers : 6.55 % Allowed : 23.65 % Favored : 69.80 % 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: -2.54 (0.37), residues: 413 helix: -5.00 (0.21), residues: 21 sheet: -0.19 (0.43), residues: 138 loop : -2.40 (0.33), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 49 HIS 0.003 0.001 HIS B 519 PHE 0.008 0.001 PHE C 100 TYR 0.010 0.001 TYR B 365 ARG 0.002 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 105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: C 62 ASN cc_start: 0.7587 (t0) cc_final: 0.7299 (t0) REVERT: B 357 ARG cc_start: 0.7963 (ttm170) cc_final: 0.6353 (mtt180) outliers start: 23 outliers final: 16 residues processed: 100 average time/residue: 0.1601 time to fit residues: 19.3453 Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.367 ------------------------------------------------------------------------------- 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 114 LEU Chi-restraints excluded: chain A residue 115 VAL 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 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 18 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.0980 chunk 32 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.119227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.104720 restraints weight = 6638.716| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.72 r_work: 0.3353 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3310 Z= 0.186 Angle : 0.616 8.229 4516 Z= 0.316 Chirality : 0.045 0.173 503 Planarity : 0.004 0.032 574 Dihedral : 4.526 20.745 460 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.54 % Favored : 93.22 % Rotamer: Outliers : 7.12 % Allowed : 23.08 % Favored : 69.80 % 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: -2.31 (0.37), residues: 413 helix: -5.05 (0.21), residues: 21 sheet: -0.07 (0.43), residues: 139 loop : -2.20 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 49 HIS 0.002 0.001 HIS B 519 PHE 0.008 0.001 PHE B 342 TYR 0.010 0.001 TYR B 365 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: 25 poor density : 80 time to evaluate : 0.363 Fit side-chains REVERT: C 62 ASN cc_start: 0.7716 (t0) cc_final: 0.7410 (t0) REVERT: B 357 ARG cc_start: 0.8014 (ttm170) cc_final: 0.6293 (mtt180) outliers start: 25 outliers final: 22 residues processed: 98 average time/residue: 0.1553 time to fit residues: 18.4236 Evaluate side-chains 99 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 53 ILE 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 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 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 22 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.0870 chunk 17 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.118389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.104100 restraints weight = 6503.276| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.68 r_work: 0.3345 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.5180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3310 Z= 0.191 Angle : 0.629 10.220 4516 Z= 0.320 Chirality : 0.045 0.172 503 Planarity : 0.004 0.032 574 Dihedral : 4.440 20.266 460 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.54 % Favored : 93.22 % Rotamer: Outliers : 7.12 % Allowed : 25.07 % Favored : 67.81 % 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: -2.18 (0.38), residues: 413 helix: -5.04 (0.21), residues: 21 sheet: 0.05 (0.44), residues: 139 loop : -2.12 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 353 HIS 0.002 0.001 HIS B 519 PHE 0.011 0.001 PHE B 342 TYR 0.011 0.001 TYR C 93 ARG 0.001 0.000 ARG A 40 *********************** 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 105 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: C 62 ASN cc_start: 0.7819 (t0) cc_final: 0.7514 (t0) REVERT: B 357 ARG cc_start: 0.7964 (ttm170) cc_final: 0.6265 (mtt180) outliers start: 25 outliers final: 25 residues processed: 97 average time/residue: 0.1598 time to fit residues: 18.4854 Evaluate side-chains 102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 77 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 53 ILE 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 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 410 ILE Chi-restraints excluded: chain B residue 418 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 524 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 36 optimal weight: 0.0770 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 0.0000 chunk 0 optimal weight: 3.9990 chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.4344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.119710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.105612 restraints weight = 6556.611| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.67 r_work: 0.3365 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.5349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3310 Z= 0.155 Angle : 0.618 9.544 4516 Z= 0.309 Chirality : 0.045 0.173 503 Planarity : 0.004 0.053 574 Dihedral : 4.218 19.137 460 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.54 % Favored : 93.22 % Rotamer: Outliers : 6.84 % Allowed : 25.36 % Favored : 67.81 % 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: -2.07 (0.38), residues: 413 helix: -5.03 (0.21), residues: 21 sheet: 0.13 (0.45), residues: 139 loop : -2.03 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 353 HIS 0.001 0.001 HIS A 99 PHE 0.009 0.001 PHE B 342 TYR 0.010 0.001 TYR C 93 ARG 0.002 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 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: C 62 ASN cc_start: 0.7810 (t0) cc_final: 0.7514 (t0) REVERT: C 95 THR cc_start: 0.9174 (t) cc_final: 0.8888 (m) REVERT: B 357 ARG cc_start: 0.7874 (ttm170) cc_final: 0.6207 (mtt180) outliers start: 24 outliers final: 20 residues processed: 93 average time/residue: 0.1625 time to fit residues: 18.0500 Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.328 ------------------------------------------------------------------------------- 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 25 SER Chi-restraints excluded: chain A residue 53 ILE 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 410 ILE Chi-restraints excluded: chain B residue 418 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 524 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.2980 chunk 22 optimal weight: 0.0170 chunk 9 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.119206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105170 restraints weight = 6525.916| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.64 r_work: 0.3358 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5485 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= 0.167 Angle : 0.627 9.089 4516 Z= 0.315 Chirality : 0.044 0.159 503 Planarity : 0.004 0.054 574 Dihedral : 4.250 18.958 460 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.05 % Favored : 93.70 % Rotamer: Outliers : 5.98 % Allowed : 26.50 % Favored : 67.52 % 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: -1.95 (0.38), residues: 413 helix: -4.99 (0.22), residues: 21 sheet: 0.21 (0.45), residues: 139 loop : -1.94 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 353 HIS 0.001 0.000 HIS A 99 PHE 0.008 0.001 PHE B 342 TYR 0.010 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 98 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 77 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 18 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7438 (mt) REVERT: C 62 ASN cc_start: 0.7788 (t0) cc_final: 0.7502 (t0) REVERT: C 95 THR cc_start: 0.9169 (t) cc_final: 0.8893 (m) REVERT: B 357 ARG cc_start: 0.7869 (ttm170) cc_final: 0.6206 (mtt180) outliers start: 21 outliers final: 19 residues processed: 91 average time/residue: 0.1653 time to fit residues: 18.2079 Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 25 SER Chi-restraints excluded: chain A residue 53 ILE 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 410 ILE Chi-restraints excluded: chain B residue 418 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 37 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 26 optimal weight: 0.0060 chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.0070 chunk 8 optimal weight: 0.0070 overall best weight: 0.2432 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.121002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.106949 restraints weight = 6324.909| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.59 r_work: 0.3390 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 3310 Z= 0.134 Angle : 0.612 8.306 4516 Z= 0.303 Chirality : 0.044 0.157 503 Planarity : 0.004 0.052 574 Dihedral : 4.012 17.614 460 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.30 % Favored : 93.46 % Rotamer: Outliers : 6.27 % Allowed : 25.64 % Favored : 68.09 % 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: -1.77 (0.39), residues: 413 helix: -4.93 (0.25), residues: 21 sheet: 0.33 (0.45), residues: 139 loop : -1.82 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP B 436 HIS 0.001 0.000 HIS A 99 PHE 0.007 0.001 PHE B 400 TYR 0.011 0.001 TYR C 93 ARG 0.002 0.000 ARG B 403 ********************** 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 100 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: C 62 ASN cc_start: 0.7768 (t0) cc_final: 0.7517 (t0) REVERT: C 95 THR cc_start: 0.9179 (t) cc_final: 0.8919 (m) REVERT: B 357 ARG cc_start: 0.7804 (ttm170) cc_final: 0.6154 (mtt180) outliers start: 22 outliers final: 20 residues processed: 93 average time/residue: 0.1505 time to fit residues: 17.0275 Evaluate side-chains 95 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.356 ------------------------------------------------------------------------------- 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 25 SER Chi-restraints excluded: chain A residue 53 ILE Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 ASP 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 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 31 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 22 optimal weight: 0.0050 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4594 ------------------------------------------------------------------------------- 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 = 0.3650 r_free = 0.3650 target = 0.119619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.105505 restraints weight = 6476.935| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.62 r_work: 0.3367 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3310 Z= 0.161 Angle : 0.643 8.988 4516 Z= 0.318 Chirality : 0.045 0.155 503 Planarity : 0.004 0.051 574 Dihedral : 4.111 17.733 460 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.81 % Favored : 93.95 % Rotamer: Outliers : 5.98 % Allowed : 26.21 % Favored : 67.81 % 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: -1.59 (0.39), residues: 413 helix: -4.70 (0.33), residues: 15 sheet: 0.41 (0.45), residues: 139 loop : -1.77 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 353 HIS 0.001 0.000 HIS B 519 PHE 0.007 0.001 PHE B 342 TYR 0.009 0.001 TYR C 93 ARG 0.003 0.000 ARG B 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2190.06 seconds wall clock time: 38 minutes 29.55 seconds (2309.55 seconds total)