Starting phenix.real_space_refine on Fri Aug 22 13:20:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvl_34131/08_2025/7yvl_34131.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvl_34131/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/7yvl_34131/08_2025/7yvl_34131.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvl_34131/08_2025/7yvl_34131.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7yvl_34131/08_2025/7yvl_34131.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvl_34131/08_2025/7yvl_34131.map" } resolution = 3.3 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= -0.001 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 2, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 17 Time building chain proxies: 1.04, per 1000 atoms: 0.32 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: 0.25 Conformation dependent library (CDL) restraints added in 173.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.07 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: 0.26 Time building geometry restraints manager: 0.34 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: 8.540 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.720 Find NCS groups from input model: 0.010 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.450 ------------------------------------------------------------------------------- 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 3316 Z= 0.718 Angle : 1.426 53.281 4528 Z= 0.828 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 : 18.50 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 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: -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 ARG 0.005 0.000 ARG B 355 TYR 0.020 0.002 TYR B 489 PHE 0.016 0.002 PHE A 106 TRP 0.028 0.003 TRP A 55 HIS 0.008 0.002 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.01093 ( 3310) covalent geometry : angle 1.16334 ( 4516) SS BOND : bond 0.03870 ( 6) SS BOND : angle 16.04889 ( 12) hydrogen bonds : bond 0.18743 ( 76) hydrogen bonds : angle 7.77322 ( 174) *********************** 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 : 0.121 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: 0.0832 time to fit residues: 11.6904 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 : 0.090 ------------------------------------------------------------------------------- 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 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 37 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: C 6 GLN B 388 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.125411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.108961 restraints weight = 6487.648| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 2.89 r_work: 0.3400 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.2921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3316 Z= 0.171 Angle : 0.749 14.046 4528 Z= 0.368 Chirality : 0.046 0.179 503 Planarity : 0.005 0.031 574 Dihedral : 5.255 44.402 462 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.02 % Favored : 92.74 % Rotamer: Outliers : 4.56 % Allowed : 21.65 % 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 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: -3.68 (0.36), residues: 413 helix: -4.74 (0.44), residues: 22 sheet: -1.71 (0.40), residues: 145 loop : -2.79 (0.34), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 68 TYR 0.018 0.002 TYR C 93 PHE 0.009 0.001 PHE B 347 TRP 0.010 0.001 TRP A 55 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 3310) covalent geometry : angle 0.73815 ( 4516) SS BOND : bond 0.00573 ( 6) SS BOND : angle 2.59169 ( 12) hydrogen bonds : bond 0.03956 ( 76) hydrogen bonds : angle 5.78284 ( 174) *********************** 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 97 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.085 Fit side-chains REVERT: A 59 LYS cc_start: 0.8372 (mtmt) cc_final: 0.8043 (mttm) REVERT: C 62 ASN cc_start: 0.7242 (t0) cc_final: 0.6971 (t0) REVERT: C 83 GLU cc_start: 0.7059 (pt0) cc_final: 0.6856 (pt0) REVERT: B 357 ARG cc_start: 0.7865 (ttm170) cc_final: 0.6530 (mtt180) REVERT: B 407 VAL cc_start: 0.9268 (OUTLIER) cc_final: 0.9050 (m) REVERT: B 467 ASP cc_start: 0.7770 (p0) cc_final: 0.7165 (p0) outliers start: 16 outliers final: 10 residues processed: 94 average time/residue: 0.0707 time to fit residues: 7.9419 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 : 0.122 ------------------------------------------------------------------------------- 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 B residue 382 VAL Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 407 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 31 optimal weight: 0.2980 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 15 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: B 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.122140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.106881 restraints weight = 6445.003| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 2.77 r_work: 0.3368 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3316 Z= 0.141 Angle : 0.652 9.528 4528 Z= 0.325 Chirality : 0.044 0.152 503 Planarity : 0.004 0.032 574 Dihedral : 4.581 23.476 460 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.78 % Favored : 92.98 % Rotamer: Outliers : 6.55 % Allowed : 21.94 % Favored : 71.51 % 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: -3.09 (0.36), residues: 413 helix: -4.77 (0.40), residues: 20 sheet: -1.13 (0.41), residues: 148 loop : -2.50 (0.34), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 40 TYR 0.011 0.001 TYR C 93 PHE 0.008 0.001 PHE B 400 TRP 0.006 0.001 TRP A 109 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 3310) covalent geometry : angle 0.64074 ( 4516) SS BOND : bond 0.01218 ( 6) SS BOND : angle 2.42855 ( 12) hydrogen bonds : bond 0.03459 ( 76) hydrogen bonds : angle 5.42493 ( 174) *********************** 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 102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.127 Fit side-chains REVERT: A 59 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8367 (mttm) REVERT: C 62 ASN cc_start: 0.7469 (t0) cc_final: 0.7173 (t0) REVERT: B 357 ARG cc_start: 0.7931 (ttm170) cc_final: 0.6502 (mtt180) REVERT: B 467 ASP cc_start: 0.7709 (p0) cc_final: 0.7117 (p0) outliers start: 23 outliers final: 18 residues processed: 96 average time/residue: 0.0638 time to fit residues: 7.3709 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 : 0.074 ------------------------------------------------------------------------------- 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 107 ASP Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 69 SER Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain B residue 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 8 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 370 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.119540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.105004 restraints weight = 6448.879| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.67 r_work: 0.3355 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3316 Z= 0.168 Angle : 0.659 10.037 4528 Z= 0.335 Chirality : 0.045 0.151 503 Planarity : 0.004 0.034 574 Dihedral : 4.791 25.771 460 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.51 % Favored : 92.25 % Rotamer: Outliers : 7.12 % Allowed : 22.79 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.76 (0.37), residues: 413 helix: -4.74 (0.35), residues: 21 sheet: -0.48 (0.42), residues: 141 loop : -2.52 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.013 0.001 TYR C 93 PHE 0.009 0.001 PHE A 24 TRP 0.007 0.001 TRP A 49 HIS 0.003 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 3310) covalent geometry : angle 0.64806 ( 4516) SS BOND : bond 0.00921 ( 6) SS BOND : angle 2.40257 ( 12) hydrogen bonds : bond 0.03496 ( 76) hydrogen bonds : angle 5.30588 ( 174) *********************** 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 106 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.129 Fit side-chains REVERT: C 55 LYS cc_start: 0.8146 (ttmm) cc_final: 0.7890 (ttmm) REVERT: C 62 ASN cc_start: 0.7674 (t0) cc_final: 0.7323 (t0) REVERT: B 357 ARG cc_start: 0.7982 (ttm170) cc_final: 0.6325 (mtt180) outliers start: 25 outliers final: 18 residues processed: 99 average time/residue: 0.0713 time to fit residues: 8.4089 Evaluate side-chains 97 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.110 ------------------------------------------------------------------------------- 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 19 THR Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 53 ILE 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 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 4 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3657 r_free = 0.3657 target = 0.120000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105518 restraints weight = 6427.715| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.69 r_work: 0.3363 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3316 Z= 0.134 Angle : 0.629 8.533 4528 Z= 0.319 Chirality : 0.044 0.170 503 Planarity : 0.004 0.032 574 Dihedral : 4.632 22.134 460 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.78 % Favored : 92.98 % Rotamer: Outliers : 7.12 % Allowed : 23.65 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.54 (0.37), residues: 413 helix: -4.75 (0.34), residues: 21 sheet: -0.28 (0.42), residues: 141 loop : -2.38 (0.33), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.014 0.001 TYR C 93 PHE 0.009 0.001 PHE A 24 TRP 0.005 0.001 TRP B 353 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 3310) covalent geometry : angle 0.62192 ( 4516) SS BOND : bond 0.00509 ( 6) SS BOND : angle 1.99007 ( 12) hydrogen bonds : bond 0.03226 ( 76) hydrogen bonds : angle 5.14787 ( 174) *********************** 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 103 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 78 time to evaluate : 0.133 Fit side-chains REVERT: A 35 SER cc_start: 0.8686 (p) cc_final: 0.8443 (t) REVERT: C 55 LYS cc_start: 0.8125 (ttmm) cc_final: 0.7913 (ttmm) REVERT: C 62 ASN cc_start: 0.7683 (t0) cc_final: 0.7358 (t0) REVERT: B 357 ARG cc_start: 0.7946 (ttm170) cc_final: 0.6323 (mtt180) outliers start: 25 outliers final: 18 residues processed: 95 average time/residue: 0.0645 time to fit residues: 7.4672 Evaluate side-chains 94 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 76 time to evaluate : 0.080 ------------------------------------------------------------------------------- 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 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 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 8 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 12 optimal weight: 0.0570 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 overall best weight: 0.5698 ------------------------------------------------------------------------------- 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 = 0.3656 r_free = 0.3656 target = 0.119817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.105442 restraints weight = 6436.734| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.67 r_work: 0.3361 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.4935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3316 Z= 0.124 Angle : 0.619 8.592 4528 Z= 0.311 Chirality : 0.044 0.166 503 Planarity : 0.004 0.031 574 Dihedral : 4.511 20.761 460 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.02 % Favored : 92.74 % Rotamer: Outliers : 7.41 % Allowed : 23.08 % Favored : 69.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.33 (0.38), residues: 413 helix: -4.85 (0.34), residues: 21 sheet: -0.09 (0.44), residues: 139 loop : -2.23 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.013 0.001 TYR C 93 PHE 0.007 0.001 PHE B 400 TRP 0.004 0.000 TRP B 353 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3310) covalent geometry : angle 0.61229 ( 4516) SS BOND : bond 0.00715 ( 6) SS BOND : angle 1.82120 ( 12) hydrogen bonds : bond 0.03045 ( 76) hydrogen bonds : angle 5.15632 ( 174) *********************** 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 108 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.122 Fit side-chains revert: symmetry clash REVERT: A 35 SER cc_start: 0.8689 (p) cc_final: 0.8461 (t) REVERT: C 62 ASN cc_start: 0.7711 (t0) cc_final: 0.7387 (t0) REVERT: B 357 ARG cc_start: 0.7979 (ttm170) cc_final: 0.6257 (mtt180) outliers start: 26 outliers final: 22 residues processed: 100 average time/residue: 0.0593 time to fit residues: 7.2145 Evaluate side-chains 101 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 79 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.1980 chunk 36 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3634 r_free = 0.3634 target = 0.118327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104151 restraints weight = 6559.368| |-----------------------------------------------------------------------------| r_work (start): 0.3425 rms_B_bonded: 2.70 r_work: 0.3341 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.5154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3316 Z= 0.150 Angle : 0.655 10.543 4528 Z= 0.330 Chirality : 0.046 0.176 503 Planarity : 0.004 0.033 574 Dihedral : 4.626 20.254 460 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.51 % Favored : 92.25 % Rotamer: Outliers : 6.55 % Allowed : 25.36 % 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 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: -2.26 (0.38), residues: 413 helix: -4.88 (0.33), residues: 21 sheet: -0.00 (0.44), residues: 139 loop : -2.20 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.013 0.001 TYR C 93 PHE 0.009 0.001 PHE A 24 TRP 0.005 0.001 TRP B 353 HIS 0.002 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 3310) covalent geometry : angle 0.64882 ( 4516) SS BOND : bond 0.00736 ( 6) SS BOND : angle 1.87406 ( 12) hydrogen bonds : bond 0.03281 ( 76) hydrogen bonds : angle 5.14229 ( 174) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 826 Ramachandran restraints generated. 413 Oldfield, 0 Emsley, 413 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 81 time to evaluate : 0.136 Fit side-chains REVERT: A 35 SER cc_start: 0.8756 (p) cc_final: 0.8473 (t) REVERT: C 62 ASN cc_start: 0.7813 (t0) cc_final: 0.7488 (t0) REVERT: B 357 ARG cc_start: 0.7980 (ttm170) cc_final: 0.6321 (mtt180) outliers start: 23 outliers final: 23 residues processed: 98 average time/residue: 0.0688 time to fit residues: 8.2094 Evaluate side-chains 102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.128 ------------------------------------------------------------------------------- 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.9990 chunk 24 optimal weight: 0.0570 chunk 33 optimal weight: 0.0770 chunk 38 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 7 optimal weight: 3.9990 chunk 14 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 27 optimal weight: 0.8980 overall best weight: 0.4856 ------------------------------------------------------------------------------- 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 = 0.3649 r_free = 0.3649 target = 0.119514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.105328 restraints weight = 6598.096| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.68 r_work: 0.3362 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3316 Z= 0.112 Angle : 0.643 9.541 4528 Z= 0.316 Chirality : 0.045 0.175 503 Planarity : 0.004 0.054 574 Dihedral : 4.396 19.073 460 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.26 % Favored : 92.49 % Rotamer: Outliers : 6.55 % Allowed : 25.36 % 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 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: -2.12 (0.38), residues: 413 helix: -4.81 (0.37), residues: 21 sheet: 0.10 (0.44), residues: 139 loop : -2.10 (0.33), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 403 TYR 0.012 0.001 TYR C 93 PHE 0.011 0.001 PHE B 342 TRP 0.004 0.000 TRP B 353 HIS 0.001 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 3310) covalent geometry : angle 0.63660 ( 4516) SS BOND : bond 0.00737 ( 6) SS BOND : angle 1.91095 ( 12) hydrogen bonds : bond 0.02993 ( 76) hydrogen bonds : angle 5.06131 ( 174) *********************** 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 98 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 0.168 Fit side-chains REVERT: A 35 SER cc_start: 0.8674 (p) cc_final: 0.8452 (t) REVERT: C 62 ASN cc_start: 0.7787 (t0) cc_final: 0.7477 (t0) REVERT: C 95 THR cc_start: 0.9158 (t) cc_final: 0.8867 (m) REVERT: B 357 ARG cc_start: 0.7880 (ttt180) cc_final: 0.6230 (mtt180) outliers start: 23 outliers final: 19 residues processed: 91 average time/residue: 0.0610 time to fit residues: 6.7696 Evaluate side-chains 92 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 0.113 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.3980 chunk 1 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.118032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.103876 restraints weight = 6563.033| |-----------------------------------------------------------------------------| r_work (start): 0.3417 rms_B_bonded: 2.68 r_work: 0.3335 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.5513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3316 Z= 0.137 Angle : 0.660 9.513 4528 Z= 0.328 Chirality : 0.045 0.159 503 Planarity : 0.004 0.053 574 Dihedral : 4.521 20.323 460 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.23 % Favored : 91.53 % 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 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: -2.06 (0.38), residues: 413 helix: -4.82 (0.37), residues: 21 sheet: 0.11 (0.44), residues: 139 loop : -2.04 (0.34), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.013 0.001 TYR C 93 PHE 0.009 0.001 PHE B 342 TRP 0.006 0.001 TRP B 353 HIS 0.001 0.001 HIS A 99 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 3310) covalent geometry : angle 0.65349 ( 4516) SS BOND : bond 0.00691 ( 6) SS BOND : angle 1.85956 ( 12) hydrogen bonds : bond 0.03118 ( 76) hydrogen bonds : angle 5.12340 ( 174) *********************** 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: 22 poor density : 76 time to evaluate : 0.105 Fit side-chains REVERT: A 35 SER cc_start: 0.8709 (p) cc_final: 0.8439 (t) REVERT: C 62 ASN cc_start: 0.7788 (t0) cc_final: 0.7492 (t0) REVERT: B 357 ARG cc_start: 0.7874 (ttt180) cc_final: 0.6091 (mtt180) outliers start: 22 outliers final: 21 residues processed: 92 average time/residue: 0.0627 time to fit residues: 6.9663 Evaluate side-chains 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 75 time to evaluate : 0.108 ------------------------------------------------------------------------------- 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 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 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 36 optimal weight: 0.0970 chunk 29 optimal weight: 0.4980 chunk 2 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 11 optimal weight: 0.7980 chunk 26 optimal weight: 0.0020 chunk 17 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 22 optimal weight: 0.0170 chunk 13 optimal weight: 2.9990 overall best weight: 0.2424 ------------------------------------------------------------------------------- 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 = 0.3669 r_free = 0.3669 target = 0.120821 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.106668 restraints weight = 6522.233| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.65 r_work: 0.3385 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3385 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3316 Z= 0.093 Angle : 0.638 8.780 4528 Z= 0.310 Chirality : 0.045 0.155 503 Planarity : 0.004 0.053 574 Dihedral : 4.132 17.192 460 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.05 % Favored : 93.70 % Rotamer: Outliers : 5.41 % Allowed : 27.07 % 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 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: -1.86 (0.39), residues: 413 helix: -4.71 (0.42), residues: 21 sheet: 0.19 (0.45), residues: 139 loop : -1.85 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 403 TYR 0.013 0.001 TYR C 93 PHE 0.007 0.001 PHE B 400 TRP 0.005 0.001 TRP B 436 HIS 0.001 0.000 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 3310) covalent geometry : angle 0.63199 ( 4516) SS BOND : bond 0.00568 ( 6) SS BOND : angle 1.79875 ( 12) hydrogen bonds : bond 0.02804 ( 76) hydrogen bonds : angle 4.97715 ( 174) ********************** 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 102 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 83 time to evaluate : 0.087 Fit side-chains REVERT: C 62 ASN cc_start: 0.7764 (t0) cc_final: 0.7502 (t0) REVERT: C 95 THR cc_start: 0.9145 (t) cc_final: 0.8888 (m) REVERT: B 357 ARG cc_start: 0.7810 (ttt180) cc_final: 0.6082 (mtt180) outliers start: 19 outliers final: 17 residues processed: 96 average time/residue: 0.0557 time to fit residues: 6.4067 Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 C residue 32 TYR 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 0 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 22 optimal weight: 0.0770 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 37 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- 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 = 0.3647 r_free = 0.3647 target = 0.119691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104973 restraints weight = 6569.594| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 2.70 r_work: 0.3359 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3316 Z= 0.125 Angle : 0.711 14.874 4528 Z= 0.338 Chirality : 0.046 0.163 503 Planarity : 0.004 0.050 574 Dihedral : 4.274 17.812 460 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.26 % Favored : 92.49 % Rotamer: Outliers : 5.13 % Allowed : 27.64 % Favored : 67.24 % 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: -1.82 (0.39), residues: 413 helix: -4.63 (0.47), residues: 19 sheet: 0.19 (0.44), residues: 139 loop : -1.84 (0.35), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 355 TYR 0.014 0.001 TYR C 93 PHE 0.010 0.001 PHE A 27 TRP 0.005 0.001 TRP B 353 HIS 0.001 0.001 HIS B 519 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 3310) covalent geometry : angle 0.70527 ( 4516) SS BOND : bond 0.00451 ( 6) SS BOND : angle 1.81895 ( 12) hydrogen bonds : bond 0.03078 ( 76) hydrogen bonds : angle 5.07562 ( 174) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1010.82 seconds wall clock time: 18 minutes 6.50 seconds (1086.50 seconds total)