Starting phenix.real_space_refine on Wed Jun 4 15:00:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wtg_32785/06_2025/7wtg_32785.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wtg_32785/06_2025/7wtg_32785.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wtg_32785/06_2025/7wtg_32785.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wtg_32785/06_2025/7wtg_32785.map" model { file = "/net/cci-nas-00/data/ceres_data/7wtg_32785/06_2025/7wtg_32785.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wtg_32785/06_2025/7wtg_32785.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 17 5.16 5 C 2107 2.51 5 N 563 2.21 5 O 631 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3318 Number of models: 1 Model: "" Number of chains: 3 Chain: "E" Number of atoms: 1612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1612 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 918 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Time building chain proxies: 3.45, per 1000 atoms: 1.04 Number of scatterers: 3318 At special positions: 0 Unit cell: (60.32, 64.48, 115.44, 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 17 16.00 O 631 8.00 N 563 7.00 C 2107 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.02 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.05 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.67 Conformation dependent library (CDL) restraints added in 372.9 milliseconds 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 778 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 8 sheets defined 5.2% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'E' and resid 337 through 343 removed outlier: 3.596A pdb=" N VAL E 341 " --> pdb=" O PRO E 337 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 403 through 405 No H-bonds generated for 'chain 'E' and resid 403 through 405' Processing helix chain 'E' and resid 406 through 411 removed outlier: 3.762A pdb=" N ILE E 410 " --> pdb=" O GLU E 406 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N ALA E 411 " --> pdb=" O VAL E 407 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 406 through 411' Processing sheet with id=AA1, first strand: chain 'E' and resid 356 through 358 removed outlier: 4.408A pdb=" N ASN E 394 " --> pdb=" O GLU E 516 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU E 516 " --> pdb=" O ASN E 394 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 58 through 60 removed outlier: 3.513A pdb=" N ASN H 59 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 5.656A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ALA H 33 " --> pdb=" O LEU H 99 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N LEU H 99 " --> pdb=" O ALA H 33 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 48 removed outlier: 7.248A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 45 through 48 removed outlier: 7.248A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 180 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: 0.75 Time building geometry restraints manager: 0.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1064 1.35 - 1.47: 930 1.47 - 1.60: 1389 1.60 - 1.73: 0 1.73 - 1.85: 21 Bond restraints: 3404 Sorted by residual: bond pdb=" N VAL E 445 " pdb=" CA VAL E 445 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.19e-02 7.06e+03 8.77e+00 bond pdb=" N LYS E 444 " pdb=" CA LYS E 444 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.21e-02 6.83e+03 7.14e+00 bond pdb=" N GLY E 447 " pdb=" CA GLY E 447 " ideal model delta sigma weight residual 1.450 1.476 -0.025 1.01e-02 9.80e+03 6.18e+00 bond pdb=" N SER E 446 " pdb=" CA SER E 446 " ideal model delta sigma weight residual 1.459 1.485 -0.026 1.21e-02 6.83e+03 4.66e+00 bond pdb=" CA VAL L 58 " pdb=" CB VAL L 58 " ideal model delta sigma weight residual 1.537 1.563 -0.026 1.29e-02 6.01e+03 4.06e+00 ... (remaining 3399 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 4350 2.34 - 4.68: 212 4.68 - 7.03: 43 7.03 - 9.37: 13 9.37 - 11.71: 2 Bond angle restraints: 4620 Sorted by residual: angle pdb=" C ILE E 410 " pdb=" N ALA E 411 " pdb=" CA ALA E 411 " ideal model delta sigma weight residual 120.60 127.40 -6.80 1.53e+00 4.27e-01 1.98e+01 angle pdb=" C GLY H 113 " pdb=" N MET H 114 " pdb=" CA MET H 114 " ideal model delta sigma weight residual 121.54 129.65 -8.11 1.91e+00 2.74e-01 1.80e+01 angle pdb=" N TYR L 94 " pdb=" CA TYR L 94 " pdb=" C TYR L 94 " ideal model delta sigma weight residual 109.81 119.12 -9.31 2.21e+00 2.05e-01 1.77e+01 angle pdb=" CA GLY E 447 " pdb=" C GLY E 447 " pdb=" O GLY E 447 " ideal model delta sigma weight residual 122.05 118.00 4.05 1.00e+00 1.00e+00 1.64e+01 angle pdb=" C GLN H 62 " pdb=" N LYS H 63 " pdb=" CA LYS H 63 " ideal model delta sigma weight residual 121.54 128.80 -7.26 1.91e+00 2.74e-01 1.44e+01 ... (remaining 4615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 1798 17.95 - 35.90: 181 35.90 - 53.84: 29 53.84 - 71.79: 4 71.79 - 89.74: 5 Dihedral angle restraints: 2017 sinusoidal: 790 harmonic: 1227 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 165.13 -72.13 1 1.00e+01 1.00e-02 6.65e+01 dihedral pdb=" CA CYS E 361 " pdb=" C CYS E 361 " pdb=" N VAL E 362 " pdb=" CA VAL E 362 " ideal model delta harmonic sigma weight residual 180.00 141.00 39.00 0 5.00e+00 4.00e-02 6.08e+01 dihedral pdb=" CA PRO E 337 " pdb=" C PRO E 337 " pdb=" N PHE E 338 " pdb=" CA PHE E 338 " ideal model delta harmonic sigma weight residual 180.00 149.52 30.48 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 2014 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 349 0.058 - 0.116: 95 0.116 - 0.174: 34 0.174 - 0.233: 8 0.233 - 0.291: 4 Chirality restraints: 490 Sorted by residual: chirality pdb=" CB THR L 85 " pdb=" CA THR L 85 " pdb=" OG1 THR L 85 " pdb=" CG2 THR L 85 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CB VAL L 58 " pdb=" CA VAL L 58 " pdb=" CG1 VAL L 58 " pdb=" CG2 VAL L 58 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA ASN E 354 " pdb=" N ASN E 354 " pdb=" C ASN E 354 " pdb=" CB ASN E 354 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.98e+00 ... (remaining 487 not shown) Planarity restraints: 601 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS E 462 " 0.053 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO E 463 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO E 463 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO E 463 " 0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 453 " 0.022 2.00e-02 2.50e+03 2.12e-02 9.01e+00 pdb=" CG TYR E 453 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TYR E 453 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TYR E 453 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR E 453 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR E 453 " 0.008 2.00e-02 2.50e+03 pdb=" CZ TYR E 453 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR E 453 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " 0.049 5.00e-02 4.00e+02 7.48e-02 8.96e+00 pdb=" N PRO L 59 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " 0.041 5.00e-02 4.00e+02 ... (remaining 598 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 922 2.82 - 3.34: 2655 3.34 - 3.86: 5232 3.86 - 4.38: 5684 4.38 - 4.90: 10127 Nonbonded interactions: 24620 Sorted by model distance: nonbonded pdb=" O SER L 60 " pdb=" OG SER L 60 " model vdw 2.297 3.040 nonbonded pdb=" O ILE L 2 " pdb=" OG1 THR L 97 " model vdw 2.349 3.040 nonbonded pdb=" NH2 ARG H 67 " pdb=" OD2 ASP H 90 " model vdw 2.364 3.120 nonbonded pdb=" OD2 ASP E 398 " pdb=" OH TYR E 423 " model vdw 2.396 3.040 nonbonded pdb=" OG1 THR L 85 " pdb=" O GLY L 101 " model vdw 2.398 3.040 ... (remaining 24615 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.130 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7115 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 : 0.006 0.050 3410 Z= 0.294 Angle : 1.208 11.712 4632 Z= 0.647 Chirality : 0.069 0.291 490 Planarity : 0.011 0.083 601 Dihedral : 14.445 89.737 1221 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.50 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.36), residues: 419 helix: -4.41 (0.43), residues: 30 sheet: -0.69 (0.47), residues: 125 loop : -2.41 (0.32), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP H 117 HIS 0.002 0.001 HIS H 106 PHE 0.035 0.004 PHE E 377 TYR 0.050 0.003 TYR E 453 ARG 0.023 0.002 ARG H 108 Details of bonding type rmsd hydrogen bonds : bond 0.14264 ( 65) hydrogen bonds : angle 9.09702 ( 180) SS BOND : bond 0.01021 ( 6) SS BOND : angle 2.82842 ( 12) covalent geometry : bond 0.00589 ( 3404) covalent geometry : angle 1.20107 ( 4620) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 386 LYS cc_start: 0.8113 (pttt) cc_final: 0.7753 (tptm) REVERT: L 27 GLN cc_start: 0.7584 (tm-30) cc_final: 0.7296 (tm-30) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.1810 time to fit residues: 18.9546 Evaluate side-chains 76 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 10 optimal weight: 0.3980 chunk 21 optimal weight: 0.0870 chunk 32 optimal weight: 0.0030 chunk 12 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 24 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.1666 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 90 GLN L 92 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.181865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.156161 restraints weight = 4298.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.156609 restraints weight = 4206.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.158165 restraints weight = 3762.115| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3410 Z= 0.117 Angle : 0.639 7.065 4632 Z= 0.331 Chirality : 0.045 0.171 490 Planarity : 0.006 0.062 601 Dihedral : 5.643 32.109 470 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.67 % Allowed : 13.33 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.69 (0.37), residues: 419 helix: -3.64 (0.71), residues: 30 sheet: -0.44 (0.48), residues: 119 loop : -2.33 (0.32), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 36 HIS 0.003 0.001 HIS E 519 PHE 0.022 0.001 PHE E 456 TYR 0.013 0.001 TYR E 501 ARG 0.005 0.001 ARG H 108 Details of bonding type rmsd hydrogen bonds : bond 0.03195 ( 65) hydrogen bonds : angle 6.21328 ( 180) SS BOND : bond 0.00532 ( 6) SS BOND : angle 1.41144 ( 12) covalent geometry : bond 0.00269 ( 3404) covalent geometry : angle 0.63556 ( 4620) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 84 average time/residue: 0.1830 time to fit residues: 18.1546 Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 76 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 432 CYS Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 65 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 13 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 0.4980 chunk 1 optimal weight: 0.4980 chunk 35 optimal weight: 0.4980 chunk 39 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 90 GLN ** 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 = 0.166308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.139040 restraints weight = 4248.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.139970 restraints weight = 3897.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.141555 restraints weight = 3628.446| |-----------------------------------------------------------------------------| r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3410 Z= 0.207 Angle : 0.712 8.438 4632 Z= 0.369 Chirality : 0.048 0.226 490 Planarity : 0.006 0.053 601 Dihedral : 5.979 35.506 470 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.50 % Allowed : 19.17 % Favored : 78.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.37), residues: 419 helix: -2.53 (1.05), residues: 24 sheet: -0.62 (0.48), residues: 117 loop : -2.12 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 36 HIS 0.001 0.000 HIS H 106 PHE 0.026 0.003 PHE H 64 TYR 0.023 0.002 TYR L 49 ARG 0.009 0.001 ARG L 30 Details of bonding type rmsd hydrogen bonds : bond 0.03275 ( 65) hydrogen bonds : angle 5.90004 ( 180) SS BOND : bond 0.00675 ( 6) SS BOND : angle 1.96755 ( 12) covalent geometry : bond 0.00484 ( 3404) covalent geometry : angle 0.70576 ( 4620) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 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: 9 poor density : 88 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 465 GLU cc_start: 0.7971 (pm20) cc_final: 0.7737 (pt0) outliers start: 9 outliers final: 6 residues processed: 90 average time/residue: 0.2119 time to fit residues: 22.1398 Evaluate side-chains 80 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 40 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 1 optimal weight: 0.4980 chunk 3 optimal weight: 0.0770 chunk 7 optimal weight: 0.0870 chunk 35 optimal weight: 0.5980 chunk 13 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.167927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.142149 restraints weight = 4294.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.142656 restraints weight = 3961.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.144293 restraints weight = 3595.310| |-----------------------------------------------------------------------------| r_work (final): 0.3639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3410 Z= 0.140 Angle : 0.639 7.352 4632 Z= 0.328 Chirality : 0.045 0.192 490 Planarity : 0.005 0.051 601 Dihedral : 5.494 33.559 470 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 2.50 % Allowed : 21.67 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.38), residues: 419 helix: -2.01 (1.13), residues: 24 sheet: -0.56 (0.47), residues: 118 loop : -1.95 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.023 0.002 PHE E 456 TYR 0.016 0.001 TYR L 94 ARG 0.004 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02881 ( 65) hydrogen bonds : angle 5.38459 ( 180) SS BOND : bond 0.00612 ( 6) SS BOND : angle 1.83069 ( 12) covalent geometry : bond 0.00333 ( 3404) covalent geometry : angle 0.63330 ( 4620) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 462 LYS cc_start: 0.8618 (mppt) cc_final: 0.8355 (mppt) REVERT: H 110 TYR cc_start: 0.7615 (t80) cc_final: 0.7341 (t80) outliers start: 9 outliers final: 5 residues processed: 82 average time/residue: 0.2121 time to fit residues: 20.2345 Evaluate side-chains 79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 26 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.0980 chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.160348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.134302 restraints weight = 4251.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.133417 restraints weight = 3699.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134762 restraints weight = 3852.124| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.3595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3410 Z= 0.226 Angle : 0.715 8.718 4632 Z= 0.373 Chirality : 0.048 0.233 490 Planarity : 0.005 0.050 601 Dihedral : 5.971 36.313 470 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 4.44 % Allowed : 20.28 % Favored : 75.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.37), residues: 419 helix: -2.93 (1.06), residues: 18 sheet: -0.81 (0.47), residues: 119 loop : -2.10 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 117 HIS 0.001 0.000 HIS H 106 PHE 0.027 0.002 PHE H 64 TYR 0.020 0.002 TYR L 49 ARG 0.005 0.001 ARG H 87 Details of bonding type rmsd hydrogen bonds : bond 0.03259 ( 65) hydrogen bonds : angle 5.50413 ( 180) SS BOND : bond 0.00714 ( 6) SS BOND : angle 2.26548 ( 12) covalent geometry : bond 0.00532 ( 3404) covalent geometry : angle 0.70701 ( 4620) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 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: 16 poor density : 82 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 8 residues processed: 92 average time/residue: 0.1957 time to fit residues: 21.0204 Evaluate side-chains 82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 26 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 21 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 90 GLN ** 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 = 0.3844 r_free = 0.3844 target = 0.163706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137739 restraints weight = 4331.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.138955 restraints weight = 3855.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.140372 restraints weight = 3476.049| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3410 Z= 0.174 Angle : 0.675 8.275 4632 Z= 0.349 Chirality : 0.047 0.217 490 Planarity : 0.006 0.054 601 Dihedral : 5.774 35.616 470 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 4.17 % Allowed : 22.78 % Favored : 73.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.37), residues: 419 helix: -2.83 (1.08), residues: 18 sheet: -0.80 (0.48), residues: 119 loop : -2.02 (0.32), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 36 HIS 0.001 0.000 HIS H 106 PHE 0.027 0.002 PHE E 456 TYR 0.014 0.001 TYR L 49 ARG 0.005 0.001 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02937 ( 65) hydrogen bonds : angle 5.24146 ( 180) SS BOND : bond 0.00739 ( 6) SS BOND : angle 2.10342 ( 12) covalent geometry : bond 0.00413 ( 3404) covalent geometry : angle 0.66773 ( 4620) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 400 PHE cc_start: 0.8840 (m-80) cc_final: 0.8605 (m-80) REVERT: E 467 ASP cc_start: 0.7783 (p0) cc_final: 0.7475 (p0) outliers start: 15 outliers final: 9 residues processed: 88 average time/residue: 0.2006 time to fit residues: 20.6357 Evaluate side-chains 83 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 26 SER Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 3.9990 chunk 39 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 10 optimal weight: 0.0970 chunk 17 optimal weight: 0.0870 overall best weight: 0.3556 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.165050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137695 restraints weight = 4280.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.138801 restraints weight = 3630.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.140352 restraints weight = 3421.485| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3410 Z= 0.159 Angle : 0.671 8.357 4632 Z= 0.348 Chirality : 0.046 0.207 490 Planarity : 0.006 0.055 601 Dihedral : 5.663 35.559 470 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.02 % Favored : 89.98 % Rotamer: Outliers : 4.17 % Allowed : 23.06 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.33 (0.38), residues: 419 helix: -2.78 (1.10), residues: 18 sheet: -0.75 (0.48), residues: 118 loop : -1.93 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 36 HIS 0.001 0.000 HIS E 519 PHE 0.028 0.002 PHE E 456 TYR 0.013 0.001 TYR L 94 ARG 0.006 0.001 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02867 ( 65) hydrogen bonds : angle 5.07989 ( 180) SS BOND : bond 0.00658 ( 6) SS BOND : angle 1.80869 ( 12) covalent geometry : bond 0.00376 ( 3404) covalent geometry : angle 0.66576 ( 4620) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 467 ASP cc_start: 0.7813 (p0) cc_final: 0.7524 (p0) outliers start: 15 outliers final: 10 residues processed: 90 average time/residue: 0.1969 time to fit residues: 20.8052 Evaluate side-chains 84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 395 VAL Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 72 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 2 optimal weight: 0.0870 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 0.0470 chunk 17 optimal weight: 0.3980 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 90 GLN ** 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 = 0.3824 r_free = 0.3824 target = 0.162338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.136344 restraints weight = 4185.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.136194 restraints weight = 3972.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.137212 restraints weight = 3770.267| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3410 Z= 0.161 Angle : 0.666 8.044 4632 Z= 0.345 Chirality : 0.047 0.212 490 Planarity : 0.005 0.054 601 Dihedral : 5.584 34.519 470 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 3.06 % Allowed : 23.61 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.38), residues: 419 helix: -2.73 (1.12), residues: 18 sheet: -0.76 (0.49), residues: 118 loop : -1.90 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 117 HIS 0.001 0.000 HIS H 106 PHE 0.029 0.002 PHE E 456 TYR 0.015 0.001 TYR L 94 ARG 0.007 0.001 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02761 ( 65) hydrogen bonds : angle 5.11923 ( 180) SS BOND : bond 0.00636 ( 6) SS BOND : angle 1.89381 ( 12) covalent geometry : bond 0.00385 ( 3404) covalent geometry : angle 0.65988 ( 4620) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 467 ASP cc_start: 0.7785 (p0) cc_final: 0.7494 (p0) outliers start: 11 outliers final: 9 residues processed: 87 average time/residue: 0.1979 time to fit residues: 20.1850 Evaluate side-chains 87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 67 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 2 optimal weight: 0.1980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 0 optimal weight: 0.2980 chunk 40 optimal weight: 0.8980 chunk 17 optimal weight: 0.0070 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 90 GLN ** 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 = 0.3853 r_free = 0.3853 target = 0.164480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.137898 restraints weight = 4234.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.137979 restraints weight = 3670.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.139349 restraints weight = 3378.714| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3410 Z= 0.156 Angle : 0.681 8.389 4632 Z= 0.353 Chirality : 0.047 0.203 490 Planarity : 0.006 0.054 601 Dihedral : 5.535 34.352 470 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.79 % Favored : 90.21 % Rotamer: Outliers : 2.78 % Allowed : 24.44 % Favored : 72.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.38), residues: 419 helix: -2.68 (1.14), residues: 18 sheet: -0.76 (0.49), residues: 118 loop : -1.87 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 117 HIS 0.001 0.000 HIS H 106 PHE 0.029 0.002 PHE E 456 TYR 0.013 0.001 TYR L 94 ARG 0.008 0.001 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02719 ( 65) hydrogen bonds : angle 5.11757 ( 180) SS BOND : bond 0.00605 ( 6) SS BOND : angle 1.88189 ( 12) covalent geometry : bond 0.00376 ( 3404) covalent geometry : angle 0.67463 ( 4620) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 467 ASP cc_start: 0.7818 (p0) cc_final: 0.7544 (p0) outliers start: 10 outliers final: 8 residues processed: 85 average time/residue: 0.1960 time to fit residues: 19.4968 Evaluate side-chains 85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 77 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 67 SER Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 9 optimal weight: 0.4980 chunk 35 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 15 optimal weight: 0.2980 chunk 20 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 90 GLN ** 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 = 0.3753 r_free = 0.3753 target = 0.156285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.130311 restraints weight = 4321.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.131612 restraints weight = 3690.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.133068 restraints weight = 3382.710| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 3410 Z= 0.210 Angle : 0.722 8.985 4632 Z= 0.376 Chirality : 0.048 0.247 490 Planarity : 0.006 0.051 601 Dihedral : 5.901 36.999 470 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.26 % Favored : 89.50 % Rotamer: Outliers : 3.06 % Allowed : 23.33 % Favored : 73.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.45 (0.38), residues: 419 helix: -2.97 (1.07), residues: 18 sheet: -0.87 (0.49), residues: 118 loop : -1.98 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP H 117 HIS 0.001 0.000 HIS H 106 PHE 0.028 0.003 PHE E 456 TYR 0.017 0.002 TYR L 94 ARG 0.008 0.001 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02868 ( 65) hydrogen bonds : angle 5.27641 ( 180) SS BOND : bond 0.00705 ( 6) SS BOND : angle 2.21061 ( 12) covalent geometry : bond 0.00501 ( 3404) covalent geometry : angle 0.71423 ( 4620) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 838 Ramachandran restraints generated. 419 Oldfield, 0 Emsley, 419 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 378 LYS cc_start: 0.8272 (tptp) cc_final: 0.7878 (tppt) REVERT: E 467 ASP cc_start: 0.7818 (p0) cc_final: 0.7502 (p0) outliers start: 11 outliers final: 9 residues processed: 84 average time/residue: 0.1990 time to fit residues: 19.6628 Evaluate side-chains 86 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 77 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 480 CYS Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain H residue 11 VAL Chi-restraints excluded: chain H residue 48 MET Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 63 SER Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 77 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 39 optimal weight: 0.5980 chunk 1 optimal weight: 0.0000 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 13 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 40 optimal weight: 0.6980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 343 ASN ** L 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** 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 = 0.3768 r_free = 0.3768 target = 0.158038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.132470 restraints weight = 4300.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.134511 restraints weight = 3405.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.134933 restraints weight = 3292.227| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.4202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3410 Z= 0.175 Angle : 0.766 11.710 4632 Z= 0.395 Chirality : 0.049 0.240 490 Planarity : 0.006 0.053 601 Dihedral : 5.801 36.212 470 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.24 % Allowed : 10.02 % Favored : 89.74 % Rotamer: Outliers : 1.94 % Allowed : 25.56 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.25 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.38), residues: 419 helix: -3.31 (0.86), residues: 24 sheet: -0.79 (0.49), residues: 118 loop : -2.03 (0.33), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 117 HIS 0.001 0.001 HIS E 519 PHE 0.029 0.002 PHE E 456 TYR 0.015 0.001 TYR L 94 ARG 0.008 0.001 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02873 ( 65) hydrogen bonds : angle 5.16921 ( 180) SS BOND : bond 0.00618 ( 6) SS BOND : angle 3.70675 ( 12) covalent geometry : bond 0.00417 ( 3404) covalent geometry : angle 0.74356 ( 4620) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1676.94 seconds wall clock time: 29 minutes 42.02 seconds (1782.02 seconds total)