Starting phenix.real_space_refine on Wed Sep 17 04:44:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ghz_51365/09_2025/9ghz_51365.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ghz_51365/09_2025/9ghz_51365.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ghz_51365/09_2025/9ghz_51365.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ghz_51365/09_2025/9ghz_51365.map" model { file = "/net/cci-nas-00/data/ceres_data/9ghz_51365/09_2025/9ghz_51365.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ghz_51365/09_2025/9ghz_51365.cif" } resolution = 3.25 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 29 5.16 5 C 2912 2.51 5 N 642 2.21 5 O 721 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4306 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3876 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 18, 'TRANS': 481} Chain breaks: 2 Chain: "A" Number of atoms: 430 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 430 Unusual residues: {'3PE': 2, 'CLR': 12} Classifications: {'undetermined': 14, 'water': 12} Link IDs: {None: 25} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 20 Time building chain proxies: 1.46, per 1000 atoms: 0.34 Number of scatterers: 4306 At special positions: 0 Unit cell: (84.032, 67.392, 69.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 2 15.00 O 721 8.00 N 642 7.00 C 2912 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 183.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 912 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 1 sheets defined 74.6% alpha, 0.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 48 through 81 removed outlier: 4.422A pdb=" N VAL A 58 " --> pdb=" O MET A 54 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N MET A 59 " --> pdb=" O HIS A 55 " (cutoff:3.500A) removed outlier: 5.378A pdb=" N THR A 74 " --> pdb=" O THR A 70 " (cutoff:3.500A) Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 83 through 87 Processing helix chain 'A' and resid 88 through 91 Processing helix chain 'A' and resid 92 through 111 removed outlier: 3.654A pdb=" N ILE A 96 " --> pdb=" O PHE A 92 " (cutoff:3.500A) Proline residue: A 103 - end of helix Processing helix chain 'A' and resid 119 through 147 removed outlier: 5.361A pdb=" N SER A 141 " --> pdb=" O PHE A 137 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ALA A 142 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 175 removed outlier: 3.635A pdb=" N ILE A 158 " --> pdb=" O GLN A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 187 Processing helix chain 'A' and resid 191 through 215 Processing helix chain 'A' and resid 222 through 227 Processing helix chain 'A' and resid 229 through 251 Processing helix chain 'A' and resid 493 through 503 Processing helix chain 'A' and resid 505 through 527 Processing helix chain 'A' and resid 528 through 536 Processing helix chain 'A' and resid 548 through 583 removed outlier: 3.547A pdb=" N GLN A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLN A 580 " --> pdb=" O SER A 576 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N LYS A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 611 Processing helix chain 'A' and resid 613 through 621 Processing helix chain 'A' and resid 622 through 643 removed outlier: 3.668A pdb=" N ILE A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) Proline residue: A 635 - end of helix Processing helix chain 'A' and resid 645 through 650 Processing helix chain 'A' and resid 659 through 690 removed outlier: 3.598A pdb=" N GLN A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N TYR A 672 " --> pdb=" O SER A 668 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY A 683 " --> pdb=" O ALA A 679 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N GLY A 684 " --> pdb=" O SER A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 693 through 713 removed outlier: 4.139A pdb=" N MET A 697 " --> pdb=" O ARG A 693 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 427 through 428 271 hydrogen bonds defined for protein. 801 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: 0.67 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 653 1.33 - 1.45: 1121 1.45 - 1.57: 2597 1.57 - 1.69: 4 1.69 - 1.81: 47 Bond restraints: 4422 Sorted by residual: bond pdb=" CB THR A 605 " pdb=" CG2 THR A 605 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.31e-01 bond pdb=" CB VAL A 165 " pdb=" CG1 VAL A 165 " ideal model delta sigma weight residual 1.521 1.499 0.022 3.30e-02 9.18e+02 4.28e-01 bond pdb=" CB LYS A 543 " pdb=" CG LYS A 543 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.14e-01 bond pdb=" N PRO A 155 " pdb=" CA PRO A 155 " ideal model delta sigma weight residual 1.469 1.477 -0.008 1.28e-02 6.10e+03 3.90e-01 bond pdb=" CB VAL A 566 " pdb=" CG2 VAL A 566 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.79e-01 ... (remaining 4417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.35: 5897 1.35 - 2.69: 129 2.69 - 4.04: 23 4.04 - 5.39: 10 5.39 - 6.74: 3 Bond angle restraints: 6062 Sorted by residual: angle pdb=" CG ARG A 441 " pdb=" CD ARG A 441 " pdb=" NE ARG A 441 " ideal model delta sigma weight residual 112.00 118.74 -6.74 2.20e+00 2.07e-01 9.37e+00 angle pdb=" CA ARG A 153 " pdb=" CB ARG A 153 " pdb=" CG ARG A 153 " ideal model delta sigma weight residual 114.10 119.91 -5.81 2.00e+00 2.50e-01 8.44e+00 angle pdb=" CA TYR A 182 " pdb=" CB TYR A 182 " pdb=" CG TYR A 182 " ideal model delta sigma weight residual 113.90 117.29 -3.39 1.80e+00 3.09e-01 3.54e+00 angle pdb=" CA LEU A 458 " pdb=" CB LEU A 458 " pdb=" CG LEU A 458 " ideal model delta sigma weight residual 116.30 122.71 -6.41 3.50e+00 8.16e-02 3.36e+00 angle pdb=" CA CYS A 437 " pdb=" CB CYS A 437 " pdb=" SG CYS A 437 " ideal model delta sigma weight residual 114.40 118.56 -4.16 2.30e+00 1.89e-01 3.26e+00 ... (remaining 6057 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 2788 17.88 - 35.75: 272 35.75 - 53.63: 79 53.63 - 71.51: 15 71.51 - 89.39: 4 Dihedral angle restraints: 3158 sinusoidal: 1725 harmonic: 1433 Sorted by residual: dihedral pdb=" CA ILE A 100 " pdb=" C ILE A 100 " pdb=" N PHE A 101 " pdb=" CA PHE A 101 " ideal model delta harmonic sigma weight residual -180.00 -162.36 -17.64 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CG ARG A 441 " pdb=" CD ARG A 441 " pdb=" NE ARG A 441 " pdb=" CZ ARG A 441 " ideal model delta sinusoidal sigma weight residual -90.00 -43.34 -46.66 2 1.50e+01 4.44e-03 1.13e+01 dihedral pdb=" CB GLU A 191 " pdb=" CG GLU A 191 " pdb=" CD GLU A 191 " pdb=" OE1 GLU A 191 " ideal model delta sinusoidal sigma weight residual 0.00 89.39 -89.39 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 3155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 474 0.030 - 0.061: 174 0.061 - 0.091: 43 0.091 - 0.122: 21 0.122 - 0.152: 5 Chirality restraints: 717 Sorted by residual: chirality pdb=" CA ARG A 153 " pdb=" N ARG A 153 " pdb=" C ARG A 153 " pdb=" CB ARG A 153 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.77e-01 chirality pdb=" CG LEU A 458 " pdb=" CB LEU A 458 " pdb=" CD1 LEU A 458 " pdb=" CD2 LEU A 458 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA VAL A 150 " pdb=" N VAL A 150 " pdb=" C VAL A 150 " pdb=" CB VAL A 150 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 ... (remaining 714 not shown) Planarity restraints: 675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 47 " 0.036 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO A 48 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 48 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 48 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 150 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 151 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 151 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 151 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 177 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO A 178 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 178 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 178 " 0.021 5.00e-02 4.00e+02 ... (remaining 672 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 292 2.74 - 3.28: 4360 3.28 - 3.82: 6944 3.82 - 4.36: 8270 4.36 - 4.90: 14428 Nonbonded interactions: 34294 Sorted by model distance: nonbonded pdb=" OD1 ASP A 110 " pdb=" NH1 ARG A 442 " model vdw 2.196 3.120 nonbonded pdb=" O ALA A 710 " pdb=" OH TYR A 716 " model vdw 2.217 3.040 nonbonded pdb=" OH TYR A 182 " pdb=" O ILE A 253 " model vdw 2.223 3.040 nonbonded pdb=" OH TYR A 87 " pdb=" OD2 ASP A 531 " model vdw 2.266 3.040 nonbonded pdb=" N GLU A 507 " pdb=" OE1 GLU A 507 " model vdw 2.277 3.120 ... (remaining 34289 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 0.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 6.710 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4422 Z= 0.116 Angle : 0.539 6.735 6062 Z= 0.266 Chirality : 0.037 0.152 717 Planarity : 0.004 0.056 675 Dihedral : 14.923 89.385 2246 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 0.24 % Allowed : 19.32 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.38), residues: 494 helix: 1.95 (0.27), residues: 358 sheet: -0.57 (1.93), residues: 10 loop : -1.37 (0.48), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 441 TYR 0.010 0.001 TYR A 636 PHE 0.017 0.001 PHE A 227 TRP 0.005 0.001 TRP A 519 HIS 0.002 0.001 HIS A 55 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 4422) covalent geometry : angle 0.53910 ( 6062) hydrogen bonds : bond 0.11730 ( 271) hydrogen bonds : angle 4.86314 ( 801) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.180 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 82 average time/residue: 0.0832 time to fit residues: 8.5883 Evaluate side-chains 73 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 0.0670 chunk 2 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.166846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.136789 restraints weight = 4997.540| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.16 r_work: 0.3181 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 4422 Z= 0.115 Angle : 0.526 5.510 6062 Z= 0.264 Chirality : 0.038 0.135 717 Planarity : 0.005 0.061 675 Dihedral : 9.256 70.321 1404 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.66 % Allowed : 16.67 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.38), residues: 494 helix: 2.07 (0.27), residues: 362 sheet: -0.48 (1.79), residues: 10 loop : -1.43 (0.49), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 441 TYR 0.010 0.001 TYR A 636 PHE 0.011 0.001 PHE A 227 TRP 0.005 0.001 TRP A 519 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 4422) covalent geometry : angle 0.52642 ( 6062) hydrogen bonds : bond 0.03962 ( 271) hydrogen bonds : angle 4.07156 ( 801) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.156 Fit side-chains REVERT: A 230 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.7469 (tp40) REVERT: A 560 MET cc_start: 0.8754 (tpp) cc_final: 0.8503 (tpp) outliers start: 11 outliers final: 7 residues processed: 91 average time/residue: 0.0682 time to fit residues: 8.0320 Evaluate side-chains 89 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 568 TYR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 685 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 22 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 21 optimal weight: 0.0070 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 49 optimal weight: 0.0020 overall best weight: 0.4806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.167785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.137611 restraints weight = 4990.819| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 2.15 r_work: 0.3231 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3074 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8341 moved from start: 0.0910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 4422 Z= 0.106 Angle : 0.505 6.222 6062 Z= 0.252 Chirality : 0.037 0.137 717 Planarity : 0.004 0.050 675 Dihedral : 8.990 74.697 1404 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.17 % Allowed : 16.43 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.38), residues: 494 helix: 2.14 (0.27), residues: 362 sheet: -0.54 (1.73), residues: 10 loop : -1.42 (0.49), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 441 TYR 0.010 0.001 TYR A 636 PHE 0.016 0.001 PHE A 132 TRP 0.005 0.001 TRP A 498 HIS 0.002 0.001 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 4422) covalent geometry : angle 0.50467 ( 6062) hydrogen bonds : bond 0.03760 ( 271) hydrogen bonds : angle 3.94801 ( 801) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8242 (tp30) cc_final: 0.7715 (tp30) REVERT: A 194 MET cc_start: 0.7936 (tmm) cc_final: 0.7663 (tmm) REVERT: A 230 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7543 (tp40) REVERT: A 560 MET cc_start: 0.8675 (tpp) cc_final: 0.8464 (tpt) outliers start: 9 outliers final: 7 residues processed: 91 average time/residue: 0.0728 time to fit residues: 8.4784 Evaluate side-chains 88 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 568 TYR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 685 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 46 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.158859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.126868 restraints weight = 4985.459| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.20 r_work: 0.3158 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4422 Z= 0.140 Angle : 0.536 6.347 6062 Z= 0.265 Chirality : 0.039 0.141 717 Planarity : 0.004 0.048 675 Dihedral : 9.029 79.251 1404 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.14 % Allowed : 16.43 % Favored : 80.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.77 (0.37), residues: 494 helix: 2.06 (0.27), residues: 362 sheet: -0.61 (1.74), residues: 10 loop : -1.45 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.013 0.001 TYR A 636 PHE 0.012 0.002 PHE A 532 TRP 0.005 0.001 TRP A 519 HIS 0.003 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 4422) covalent geometry : angle 0.53584 ( 6062) hydrogen bonds : bond 0.04020 ( 271) hydrogen bonds : angle 4.02335 ( 801) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.094 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8412 (tp30) cc_final: 0.7952 (tp30) REVERT: A 230 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.7592 (tp40) outliers start: 13 outliers final: 10 residues processed: 88 average time/residue: 0.0667 time to fit residues: 7.6381 Evaluate side-chains 92 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 568 TYR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 685 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.166441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.135858 restraints weight = 4914.116| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 2.21 r_work: 0.3234 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.1045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4422 Z= 0.121 Angle : 0.531 6.666 6062 Z= 0.261 Chirality : 0.038 0.141 717 Planarity : 0.004 0.047 675 Dihedral : 8.986 83.391 1404 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.38 % Allowed : 16.91 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.37), residues: 494 helix: 2.11 (0.27), residues: 362 sheet: -0.62 (1.70), residues: 10 loop : -1.43 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 153 TYR 0.012 0.001 TYR A 636 PHE 0.038 0.002 PHE A 132 TRP 0.005 0.001 TRP A 519 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00275 ( 4422) covalent geometry : angle 0.53084 ( 6062) hydrogen bonds : bond 0.03891 ( 271) hydrogen bonds : angle 3.98892 ( 801) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 GLU cc_start: 0.8486 (tp30) cc_final: 0.7949 (tp30) REVERT: A 230 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7660 (tp40) REVERT: A 629 MET cc_start: 0.8301 (tmm) cc_final: 0.7766 (ttp) outliers start: 14 outliers final: 10 residues processed: 92 average time/residue: 0.0680 time to fit residues: 8.1833 Evaluate side-chains 95 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 568 TYR Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 687 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 1 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.3980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.166564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.136110 restraints weight = 5101.111| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.18 r_work: 0.3352 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3193 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4422 Z= 0.118 Angle : 0.532 6.893 6062 Z= 0.265 Chirality : 0.039 0.145 717 Planarity : 0.004 0.048 675 Dihedral : 8.941 89.583 1404 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.38 % Allowed : 15.94 % Favored : 80.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.37), residues: 494 helix: 2.11 (0.27), residues: 362 sheet: -0.58 (1.65), residues: 10 loop : -1.41 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.012 0.001 TYR A 636 PHE 0.034 0.002 PHE A 132 TRP 0.005 0.001 TRP A 519 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 4422) covalent geometry : angle 0.53206 ( 6062) hydrogen bonds : bond 0.03863 ( 271) hydrogen bonds : angle 3.95263 ( 801) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 150 VAL cc_start: 0.7114 (OUTLIER) cc_final: 0.6673 (m) REVERT: A 191 GLU cc_start: 0.8502 (tp30) cc_final: 0.8077 (tp30) REVERT: A 230 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7673 (tp40) outliers start: 14 outliers final: 11 residues processed: 88 average time/residue: 0.0711 time to fit residues: 8.1041 Evaluate side-chains 93 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 568 TYR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 685 VAL Chi-restraints excluded: chain A residue 687 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 41 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.0170 chunk 9 optimal weight: 3.9990 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.164968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.134203 restraints weight = 5060.429| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.19 r_work: 0.3359 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 4422 Z= 0.113 Angle : 0.531 7.395 6062 Z= 0.262 Chirality : 0.038 0.144 717 Planarity : 0.004 0.049 675 Dihedral : 8.682 79.569 1404 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.38 % Allowed : 16.67 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.37), residues: 494 helix: 2.08 (0.27), residues: 362 sheet: -0.28 (1.61), residues: 10 loop : -1.38 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.011 0.001 TYR A 636 PHE 0.032 0.002 PHE A 132 TRP 0.005 0.001 TRP A 519 HIS 0.002 0.001 HIS A 249 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 4422) covalent geometry : angle 0.53125 ( 6062) hydrogen bonds : bond 0.03754 ( 271) hydrogen bonds : angle 3.93851 ( 801) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.159 Fit side-chains revert: symmetry clash REVERT: A 150 VAL cc_start: 0.7125 (OUTLIER) cc_final: 0.6688 (m) REVERT: A 194 MET cc_start: 0.7864 (tmm) cc_final: 0.7647 (ptm) REVERT: A 230 GLN cc_start: 0.8861 (OUTLIER) cc_final: 0.7656 (tp40) REVERT: A 535 GLN cc_start: 0.8341 (OUTLIER) cc_final: 0.8016 (mm-40) outliers start: 14 outliers final: 9 residues processed: 90 average time/residue: 0.0731 time to fit residues: 8.4979 Evaluate side-chains 95 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 568 TYR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 685 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 3 optimal weight: 0.2980 chunk 4 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 41 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.162349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.130991 restraints weight = 4999.851| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 2.19 r_work: 0.3390 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4422 Z= 0.118 Angle : 0.527 7.184 6062 Z= 0.263 Chirality : 0.039 0.149 717 Planarity : 0.004 0.047 675 Dihedral : 8.555 72.216 1404 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.38 % Allowed : 17.15 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.37), residues: 494 helix: 2.06 (0.27), residues: 362 sheet: -0.41 (1.55), residues: 10 loop : -1.38 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 153 TYR 0.012 0.001 TYR A 636 PHE 0.029 0.002 PHE A 132 TRP 0.005 0.001 TRP A 519 HIS 0.002 0.001 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 4422) covalent geometry : angle 0.52676 ( 6062) hydrogen bonds : bond 0.03810 ( 271) hydrogen bonds : angle 3.95751 ( 801) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.155 Fit side-chains revert: symmetry clash REVERT: A 150 VAL cc_start: 0.7096 (OUTLIER) cc_final: 0.6656 (m) REVERT: A 194 MET cc_start: 0.7898 (tmm) cc_final: 0.7610 (ptm) REVERT: A 230 GLN cc_start: 0.8866 (OUTLIER) cc_final: 0.7659 (tp40) REVERT: A 535 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8022 (mm-40) outliers start: 14 outliers final: 9 residues processed: 87 average time/residue: 0.0722 time to fit residues: 8.1018 Evaluate side-chains 92 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 504 MET Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 568 TYR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 685 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 0.7980 chunk 30 optimal weight: 0.0980 chunk 36 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.168578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.137984 restraints weight = 5020.166| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.23 r_work: 0.3170 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 4422 Z= 0.115 Angle : 0.526 7.290 6062 Z= 0.264 Chirality : 0.038 0.153 717 Planarity : 0.004 0.047 675 Dihedral : 8.450 64.111 1404 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.14 % Allowed : 17.15 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.37), residues: 494 helix: 2.15 (0.27), residues: 356 sheet: -0.37 (1.55), residues: 10 loop : -1.41 (0.47), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 153 TYR 0.012 0.001 TYR A 636 PHE 0.027 0.002 PHE A 132 TRP 0.005 0.001 TRP A 519 HIS 0.002 0.001 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 4422) covalent geometry : angle 0.52587 ( 6062) hydrogen bonds : bond 0.03776 ( 271) hydrogen bonds : angle 3.94805 ( 801) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.133 Fit side-chains revert: symmetry clash REVERT: A 150 VAL cc_start: 0.7133 (OUTLIER) cc_final: 0.6698 (m) REVERT: A 194 MET cc_start: 0.7777 (tmm) cc_final: 0.7462 (ptm) REVERT: A 230 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7504 (tp40) REVERT: A 535 GLN cc_start: 0.8255 (OUTLIER) cc_final: 0.7923 (mm-40) outliers start: 13 outliers final: 9 residues processed: 88 average time/residue: 0.0669 time to fit residues: 7.6179 Evaluate side-chains 93 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 568 TYR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 685 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 10.0000 chunk 6 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 36 optimal weight: 7.9990 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 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 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.163930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.132896 restraints weight = 4999.250| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 2.18 r_work: 0.3311 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4422 Z= 0.128 Angle : 0.547 7.407 6062 Z= 0.272 Chirality : 0.039 0.152 717 Planarity : 0.004 0.048 675 Dihedral : 8.459 58.540 1404 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.90 % Allowed : 17.63 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.37), residues: 494 helix: 2.00 (0.27), residues: 362 sheet: -0.37 (1.56), residues: 10 loop : -1.38 (0.48), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 153 TYR 0.013 0.001 TYR A 636 PHE 0.027 0.002 PHE A 132 TRP 0.004 0.001 TRP A 52 HIS 0.003 0.001 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 4422) covalent geometry : angle 0.54667 ( 6062) hydrogen bonds : bond 0.03927 ( 271) hydrogen bonds : angle 4.01600 ( 801) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 150 VAL cc_start: 0.7143 (OUTLIER) cc_final: 0.6697 (m) REVERT: A 194 MET cc_start: 0.7882 (tmm) cc_final: 0.7517 (ptm) REVERT: A 230 GLN cc_start: 0.8860 (OUTLIER) cc_final: 0.7665 (tp40) REVERT: A 535 GLN cc_start: 0.8365 (OUTLIER) cc_final: 0.8033 (mm-40) outliers start: 12 outliers final: 9 residues processed: 90 average time/residue: 0.0707 time to fit residues: 8.2519 Evaluate side-chains 96 residues out of total 414 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 141 SER Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 230 GLN Chi-restraints excluded: chain A residue 453 ARG Chi-restraints excluded: chain A residue 535 GLN Chi-restraints excluded: chain A residue 539 GLU Chi-restraints excluded: chain A residue 568 TYR Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 614 VAL Chi-restraints excluded: chain A residue 649 ILE Chi-restraints excluded: chain A residue 685 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.0770 chunk 21 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 2 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.167590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.137589 restraints weight = 4976.772| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.15 r_work: 0.3400 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4422 Z= 0.116 Angle : 0.534 7.320 6062 Z= 0.268 Chirality : 0.039 0.150 717 Planarity : 0.005 0.048 675 Dihedral : 8.322 59.318 1404 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.90 % Allowed : 17.63 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.83 (0.37), residues: 494 helix: 2.13 (0.27), residues: 356 sheet: -0.34 (1.54), residues: 10 loop : -1.37 (0.48), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 153 TYR 0.011 0.001 TYR A 636 PHE 0.026 0.002 PHE A 132 TRP 0.006 0.001 TRP A 52 HIS 0.002 0.001 HIS A 643 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 4422) covalent geometry : angle 0.53417 ( 6062) hydrogen bonds : bond 0.03799 ( 271) hydrogen bonds : angle 3.97560 ( 801) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1280.34 seconds wall clock time: 22 minutes 41.68 seconds (1361.68 seconds total)