Starting phenix.real_space_refine on Wed Sep 17 03:18:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cah_30331/09_2025/7cah_30331.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cah_30331/09_2025/7cah_30331.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7cah_30331/09_2025/7cah_30331.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cah_30331/09_2025/7cah_30331.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cah_30331/09_2025/7cah_30331.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cah_30331/09_2025/7cah_30331.map" } resolution = 3.9 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= 0.212 sd= 3.720 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 7 5.16 5 C 1842 2.51 5 N 473 2.21 5 O 567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2889 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 704 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 6, 'TRANS': 98} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 158 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 5, 'GLU:plan': 3, 'ARG:plan': 2, 'HIS:plan': 1, 'TYR:plan': 1, 'PHE:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 66 Chain: "E" Number of atoms: 903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 903 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 4, 'TRANS': 115} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1282 Classifications: {'peptide': 179} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 10, 'TRANS': 168} Chain breaks: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 202 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 6, 'PHE:plan': 3, 'ASN:plan1': 2, 'TYR:plan': 4, 'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 105 Time building chain proxies: 1.04, per 1000 atoms: 0.36 Number of scatterers: 2889 At special positions: 0 Unit cell: (68.64, 72.8, 64.48, 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 7 16.00 O 567 8.00 N 473 7.00 C 1842 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 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: 0.28 Conformation dependent library (CDL) restraints added in 158.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 7 sheets defined 11.9% alpha, 27.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 364 through 372 removed outlier: 3.717A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ALA A 372 " --> pdb=" O LEU A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.618A pdb=" N ASN A 388 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASP A 389 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.741A pdb=" N VAL D 12 " --> pdb=" O GLU D 104 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 18 through 22 Processing sheet with id=AA3, first strand: chain 'D' and resid 52 through 53 removed outlier: 5.155A pdb=" N SER D 42 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N LYS D 38 " --> pdb=" O SER D 42 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N TRP D 34 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12 removed outlier: 5.748A pdb=" N LYS E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N TRP E 47 " --> pdb=" O LYS E 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 96 hydrogen bonds defined for protein. 213 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: 0.31 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 923 1.34 - 1.46: 741 1.46 - 1.58: 1294 1.58 - 1.70: 0 1.70 - 1.82: 7 Bond restraints: 2965 Sorted by residual: bond pdb=" C ILE E 51 " pdb=" N ASP E 52 " ideal model delta sigma weight residual 1.330 1.269 0.061 1.47e-02 4.63e+03 1.73e+01 bond pdb=" C ASP E 102 " pdb=" N PRO E 103 " ideal model delta sigma weight residual 1.334 1.359 -0.025 2.34e-02 1.83e+03 1.11e+00 bond pdb=" C THR A 430 " pdb=" N GLY A 431 " ideal model delta sigma weight residual 1.328 1.338 -0.010 1.13e-02 7.83e+03 8.60e-01 bond pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 1.458 1.447 0.011 1.19e-02 7.06e+03 8.56e-01 bond pdb=" CB TRP D 93 " pdb=" CG TRP D 93 " ideal model delta sigma weight residual 1.498 1.470 0.028 3.10e-02 1.04e+03 8.43e-01 ... (remaining 2960 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.73: 4033 3.73 - 7.45: 29 7.45 - 11.18: 1 11.18 - 14.91: 0 14.91 - 18.63: 1 Bond angle restraints: 4064 Sorted by residual: angle pdb=" CA CYS A 432 " pdb=" CB CYS A 432 " pdb=" SG CYS A 432 " ideal model delta sigma weight residual 114.40 123.14 -8.74 2.30e+00 1.89e-01 1.44e+01 angle pdb=" C LYS A 378 " pdb=" N CYS A 379 " pdb=" CA CYS A 379 " ideal model delta sigma weight residual 123.00 118.23 4.77 1.41e+00 5.03e-01 1.14e+01 angle pdb=" C LYS E 12 " pdb=" N LYS E 13 " pdb=" CA LYS E 13 " ideal model delta sigma weight residual 120.81 139.44 -18.63 5.77e+00 3.00e-02 1.04e+01 angle pdb=" C ILE E 51 " pdb=" N ASP E 52 " pdb=" CA ASP E 52 " ideal model delta sigma weight residual 120.68 115.86 4.82 1.52e+00 4.33e-01 1.00e+01 angle pdb=" N HIS A 519 " pdb=" CA HIS A 519 " pdb=" C HIS A 519 " ideal model delta sigma weight residual 114.09 109.34 4.75 1.55e+00 4.16e-01 9.40e+00 ... (remaining 4059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.51: 1503 15.51 - 31.02: 170 31.02 - 46.53: 33 46.53 - 62.04: 1 62.04 - 77.55: 3 Dihedral angle restraints: 1710 sinusoidal: 535 harmonic: 1175 Sorted by residual: dihedral pdb=" CA ASP E 102 " pdb=" C ASP E 102 " pdb=" N PRO E 103 " pdb=" CA PRO E 103 " ideal model delta harmonic sigma weight residual -180.00 -137.55 -42.45 0 5.00e+00 4.00e-02 7.21e+01 dihedral pdb=" CA CYS A 432 " pdb=" C CYS A 432 " pdb=" N VAL A 433 " pdb=" CA VAL A 433 " ideal model delta harmonic sigma weight residual -180.00 -149.72 -30.28 0 5.00e+00 4.00e-02 3.67e+01 dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 149.85 30.15 0 5.00e+00 4.00e-02 3.64e+01 ... (remaining 1707 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 259 0.033 - 0.065: 116 0.065 - 0.098: 48 0.098 - 0.131: 23 0.131 - 0.163: 7 Chirality restraints: 453 Sorted by residual: chirality pdb=" CA CYS A 432 " pdb=" N CYS A 432 " pdb=" C CYS A 432 " pdb=" CB CYS A 432 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.68e-01 chirality pdb=" CA VAL D 12 " pdb=" N VAL D 12 " pdb=" C VAL D 12 " pdb=" CB VAL D 12 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.81e-01 chirality pdb=" CA ILE A 434 " pdb=" N ILE A 434 " pdb=" C ILE A 434 " pdb=" CB ILE A 434 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 ... (remaining 450 not shown) Planarity restraints: 531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 102 " -0.041 5.00e-02 4.00e+02 6.17e-02 6.10e+00 pdb=" N PRO E 103 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 103 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 103 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 412 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 520 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.75e+00 pdb=" N PRO A 521 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 521 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 521 " 0.023 5.00e-02 4.00e+02 ... (remaining 528 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 127 2.69 - 3.24: 3052 3.24 - 3.79: 4383 3.79 - 4.35: 5694 4.35 - 4.90: 9144 Nonbonded interactions: 22400 Sorted by model distance: nonbonded pdb=" OG SER E 119 " pdb=" O ALA E 121 " model vdw 2.137 3.040 nonbonded pdb=" O ASP E 102 " pdb=" N TYR E 104 " model vdw 2.222 3.120 nonbonded pdb=" OD2 ASP E 60 " pdb=" NZ LYS E 65 " model vdw 2.242 3.120 nonbonded pdb=" OD1 ASN A 437 " pdb=" N SER A 438 " model vdw 2.297 3.120 nonbonded pdb=" O SER E 85 " pdb=" OG SER E 85 " model vdw 2.336 3.040 ... (remaining 22395 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: 0.530 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: 0.050 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.990 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6521 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 : 0.005 0.061 2968 Z= 0.253 Angle : 0.923 18.632 4070 Z= 0.509 Chirality : 0.050 0.163 453 Planarity : 0.006 0.062 531 Dihedral : 13.676 77.553 951 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 18.79 Ramachandran Plot: Outliers : 0.25 % Allowed : 19.95 % Favored : 79.80 % Rotamer: Outliers : 0.00 % Allowed : 10.37 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.53 % 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: -5.76 (0.31), residues: 396 helix: -4.70 (0.25), residues: 39 sheet: -3.12 (0.39), residues: 117 loop : -4.25 (0.30), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG E 87 TYR 0.017 0.002 TYR E 32 PHE 0.024 0.002 PHE D 82 TRP 0.016 0.002 TRP E 110 HIS 0.005 0.003 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00490 ( 2965) covalent geometry : angle 0.92074 ( 4064) SS BOND : bond 0.01309 ( 3) SS BOND : angle 1.98506 ( 6) hydrogen bonds : bond 0.16151 ( 90) hydrogen bonds : angle 10.18766 ( 213) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.120 Fit side-chains REVERT: A 340 GLU cc_start: 0.6417 (pp20) cc_final: 0.6041 (pp20) outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.0428 time to fit residues: 2.4208 Evaluate side-chains 24 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 9.9990 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 0.0170 chunk 37 optimal weight: 0.0470 overall best weight: 0.4316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.091964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.086918 restraints weight = 12411.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.087227 restraints weight = 11292.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.087318 restraints weight = 10142.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.087323 restraints weight = 9646.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.087323 restraints weight = 9620.883| |-----------------------------------------------------------------------------| r_work (final): 0.3842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6447 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2968 Z= 0.131 Angle : 0.722 15.328 4070 Z= 0.365 Chirality : 0.048 0.211 453 Planarity : 0.006 0.055 531 Dihedral : 6.676 47.713 430 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.35 % Favored : 89.65 % Rotamer: Outliers : 2.22 % Allowed : 13.70 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.76 (0.35), residues: 396 helix: -3.68 (0.51), residues: 39 sheet: -2.50 (0.41), residues: 119 loop : -3.58 (0.34), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.012 0.002 TYR A 365 PHE 0.017 0.001 PHE D 82 TRP 0.017 0.002 TRP E 110 HIS 0.009 0.003 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2965) covalent geometry : angle 0.71949 ( 4064) SS BOND : bond 0.01154 ( 3) SS BOND : angle 1.59150 ( 6) hydrogen bonds : bond 0.03382 ( 90) hydrogen bonds : angle 7.84170 ( 213) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 340 GLU cc_start: 0.6561 (pp20) cc_final: 0.6187 (pp20) outliers start: 6 outliers final: 2 residues processed: 45 average time/residue: 0.0515 time to fit residues: 2.9864 Evaluate side-chains 32 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 28 optimal weight: 0.0470 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 37 optimal weight: 0.0870 overall best weight: 0.8060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.092319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.087652 restraints weight = 12553.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.087930 restraints weight = 11378.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.088071 restraints weight = 10456.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.088344 restraints weight = 9760.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.088400 restraints weight = 9183.751| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6409 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2968 Z= 0.126 Angle : 0.687 13.629 4070 Z= 0.350 Chirality : 0.048 0.174 453 Planarity : 0.005 0.051 531 Dihedral : 6.354 41.800 430 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 2.59 % Allowed : 15.56 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.30 (0.37), residues: 396 helix: -3.25 (0.63), residues: 39 sheet: -2.19 (0.43), residues: 120 loop : -3.28 (0.36), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 87 TYR 0.010 0.001 TYR E 50 PHE 0.017 0.002 PHE E 54 TRP 0.011 0.002 TRP E 110 HIS 0.004 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 2965) covalent geometry : angle 0.68572 ( 4064) SS BOND : bond 0.00652 ( 3) SS BOND : angle 1.24692 ( 6) hydrogen bonds : bond 0.03407 ( 90) hydrogen bonds : angle 7.63563 ( 213) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.6583 (pp20) cc_final: 0.6254 (pp20) outliers start: 7 outliers final: 3 residues processed: 39 average time/residue: 0.0588 time to fit residues: 2.9535 Evaluate side-chains 32 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 29 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 40.0000 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3940 r_free = 0.3940 target = 0.091748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.086563 restraints weight = 12507.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.086978 restraints weight = 10855.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.087338 restraints weight = 9623.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.087338 restraints weight = 8694.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.087338 restraints weight = 8694.166| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.2511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2968 Z= 0.139 Angle : 0.691 15.174 4070 Z= 0.348 Chirality : 0.047 0.164 453 Planarity : 0.006 0.053 531 Dihedral : 6.239 42.629 430 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Rotamer: Outliers : 3.70 % Allowed : 16.67 % Favored : 79.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -4.07 (0.38), residues: 396 helix: -3.30 (0.62), residues: 39 sheet: -1.92 (0.44), residues: 120 loop : -3.16 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 87 TYR 0.009 0.001 TYR E 50 PHE 0.016 0.002 PHE D 82 TRP 0.011 0.002 TRP E 110 HIS 0.004 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2965) covalent geometry : angle 0.68801 ( 4064) SS BOND : bond 0.01143 ( 3) SS BOND : angle 1.68969 ( 6) hydrogen bonds : bond 0.03441 ( 90) hydrogen bonds : angle 7.57473 ( 213) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 340 GLU cc_start: 0.6615 (pp20) cc_final: 0.6222 (pp20) outliers start: 10 outliers final: 5 residues processed: 39 average time/residue: 0.0431 time to fit residues: 2.2086 Evaluate side-chains 35 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 30 time to evaluate : 0.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain A residue 376 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 32 optimal weight: 0.0270 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 30.0000 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.092434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.087374 restraints weight = 12295.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.087749 restraints weight = 10837.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.088102 restraints weight = 9708.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.088352 restraints weight = 8757.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.088352 restraints weight = 8091.395| |-----------------------------------------------------------------------------| r_work (final): 0.3861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2968 Z= 0.127 Angle : 0.675 14.330 4070 Z= 0.341 Chirality : 0.047 0.153 453 Planarity : 0.005 0.053 531 Dihedral : 6.053 40.006 430 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Rotamer: Outliers : 4.44 % Allowed : 17.04 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.93 (0.38), residues: 396 helix: -3.36 (0.57), residues: 39 sheet: -1.73 (0.45), residues: 120 loop : -3.09 (0.37), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 87 TYR 0.009 0.001 TYR E 50 PHE 0.015 0.001 PHE D 82 TRP 0.010 0.001 TRP E 110 HIS 0.004 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2965) covalent geometry : angle 0.67361 ( 4064) SS BOND : bond 0.00615 ( 3) SS BOND : angle 1.28837 ( 6) hydrogen bonds : bond 0.03237 ( 90) hydrogen bonds : angle 7.36073 ( 213) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 35 time to evaluate : 0.135 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 43 average time/residue: 0.0478 time to fit residues: 2.7142 Evaluate side-chains 40 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 48 ILE Chi-restraints excluded: chain E residue 102 ASP Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain A residue 362 VAL Chi-restraints excluded: chain A residue 376 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 1.9990 chunk 8 optimal weight: 10.0000 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.088762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.084546 restraints weight = 12962.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.084737 restraints weight = 12044.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.084830 restraints weight = 11292.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.084835 restraints weight = 10741.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.085005 restraints weight = 10701.733| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.2430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 2968 Z= 0.263 Angle : 0.816 17.018 4070 Z= 0.417 Chirality : 0.050 0.160 453 Planarity : 0.006 0.059 531 Dihedral : 7.201 43.209 430 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.94 % Favored : 81.06 % Rotamer: Outliers : 4.81 % Allowed : 17.78 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.26 % 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: -4.37 (0.37), residues: 396 helix: -3.81 (0.51), residues: 33 sheet: -2.22 (0.42), residues: 124 loop : -3.29 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 87 TYR 0.015 0.002 TYR A 380 PHE 0.021 0.002 PHE D 82 TRP 0.012 0.002 TRP E 110 HIS 0.006 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00577 ( 2965) covalent geometry : angle 0.81212 ( 4064) SS BOND : bond 0.01309 ( 3) SS BOND : angle 2.18107 ( 6) hydrogen bonds : bond 0.04110 ( 90) hydrogen bonds : angle 8.25197 ( 213) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 33 time to evaluate : 0.112 Fit side-chains REVERT: D 99 GLN cc_start: 0.6400 (OUTLIER) cc_final: 0.6194 (pt0) outliers start: 13 outliers final: 9 residues processed: 43 average time/residue: 0.0481 time to fit residues: 2.7150 Evaluate side-chains 39 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 29 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 20 ILE Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 99 GLN Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain A residue 376 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 2 optimal weight: 9.9990 chunk 25 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 7 optimal weight: 20.0000 chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 5 optimal weight: 8.9990 chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 6.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.092876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.087493 restraints weight = 12499.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.088002 restraints weight = 10828.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.088002 restraints weight = 9520.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.088002 restraints weight = 9520.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.088002 restraints weight = 9520.893| |-----------------------------------------------------------------------------| r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6502 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2968 Z= 0.124 Angle : 0.703 15.571 4070 Z= 0.353 Chirality : 0.047 0.168 453 Planarity : 0.006 0.051 531 Dihedral : 6.193 45.479 430 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.10 % Favored : 89.90 % Rotamer: Outliers : 2.22 % Allowed : 20.37 % Favored : 77.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.96 (0.38), residues: 396 helix: -3.55 (0.54), residues: 33 sheet: -1.83 (0.44), residues: 120 loop : -3.06 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 98 TYR 0.013 0.001 TYR E 50 PHE 0.014 0.001 PHE D 82 TRP 0.009 0.001 TRP E 110 HIS 0.005 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 2965) covalent geometry : angle 0.70105 ( 4064) SS BOND : bond 0.01208 ( 3) SS BOND : angle 1.47274 ( 6) hydrogen bonds : bond 0.03111 ( 90) hydrogen bonds : angle 7.45674 ( 213) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.116 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 43 average time/residue: 0.0546 time to fit residues: 3.0129 Evaluate side-chains 35 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 20 optimal weight: 0.9990 chunk 32 optimal weight: 0.0970 chunk 36 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 33 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.093755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.089649 restraints weight = 12570.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.089540 restraints weight = 15222.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.089970 restraints weight = 12960.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.089933 restraints weight = 9911.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.090036 restraints weight = 10170.868| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6359 moved from start: 0.3493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2968 Z= 0.118 Angle : 0.675 14.523 4070 Z= 0.340 Chirality : 0.047 0.166 453 Planarity : 0.006 0.058 531 Dihedral : 5.899 43.063 430 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 1.48 % Allowed : 21.48 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.78 (0.38), residues: 396 helix: -3.31 (0.57), residues: 39 sheet: -1.65 (0.45), residues: 122 loop : -2.97 (0.38), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 87 TYR 0.009 0.001 TYR E 50 PHE 0.013 0.001 PHE A 515 TRP 0.010 0.001 TRP E 110 HIS 0.004 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 2965) covalent geometry : angle 0.67344 ( 4064) SS BOND : bond 0.01101 ( 3) SS BOND : angle 1.46959 ( 6) hydrogen bonds : bond 0.03018 ( 90) hydrogen bonds : angle 7.18958 ( 213) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 36 time to evaluate : 0.121 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 40 average time/residue: 0.0424 time to fit residues: 2.3082 Evaluate side-chains 33 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 30 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 15 optimal weight: 10.0000 chunk 1 optimal weight: 0.0370 chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 23 optimal weight: 8.9990 chunk 25 optimal weight: 0.7980 chunk 30 optimal weight: 8.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.094198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.088486 restraints weight = 12594.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.088910 restraints weight = 11065.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.089259 restraints weight = 9931.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.089366 restraints weight = 9046.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 17)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.089543 restraints weight = 8578.275| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6432 moved from start: 0.3678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2968 Z= 0.126 Angle : 0.708 14.032 4070 Z= 0.359 Chirality : 0.048 0.162 453 Planarity : 0.006 0.061 531 Dihedral : 5.884 40.582 430 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 1.48 % Allowed : 22.59 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.26 % 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: -3.64 (0.39), residues: 396 helix: -3.41 (0.56), residues: 39 sheet: -1.60 (0.44), residues: 124 loop : -2.80 (0.39), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG E 87 TYR 0.009 0.001 TYR E 50 PHE 0.010 0.001 PHE D 82 TRP 0.010 0.001 TRP E 110 HIS 0.003 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 2965) covalent geometry : angle 0.70514 ( 4064) SS BOND : bond 0.01047 ( 3) SS BOND : angle 1.72086 ( 6) hydrogen bonds : bond 0.03010 ( 90) hydrogen bonds : angle 7.23357 ( 213) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 34 time to evaluate : 0.080 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.0420 time to fit residues: 2.1853 Evaluate side-chains 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.090713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.085757 restraints weight = 12810.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.085957 restraints weight = 11530.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.085957 restraints weight = 10693.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.085957 restraints weight = 10693.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.085957 restraints weight = 10693.748| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6597 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 2968 Z= 0.204 Angle : 0.768 15.355 4070 Z= 0.392 Chirality : 0.049 0.159 453 Planarity : 0.006 0.060 531 Dihedral : 6.597 43.438 430 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 1.85 % Allowed : 21.48 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.87 (0.39), residues: 396 helix: -3.72 (0.54), residues: 33 sheet: -1.84 (0.44), residues: 125 loop : -2.93 (0.39), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 87 TYR 0.012 0.002 TYR A 380 PHE 0.015 0.002 PHE D 82 TRP 0.010 0.002 TRP E 110 HIS 0.006 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00448 ( 2965) covalent geometry : angle 0.76604 ( 4064) SS BOND : bond 0.01565 ( 3) SS BOND : angle 1.46292 ( 6) hydrogen bonds : bond 0.03603 ( 90) hydrogen bonds : angle 7.81130 ( 213) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 792 Ramachandran restraints generated. 396 Oldfield, 0 Emsley, 396 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.071 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 38 average time/residue: 0.0417 time to fit residues: 2.1301 Evaluate side-chains 34 residues out of total 351 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 31 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 5 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 106 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 10.0000 chunk 29 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 9 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.091731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.086279 restraints weight = 12575.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 21)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.086367 restraints weight = 11468.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.086367 restraints weight = 11029.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.086367 restraints weight = 11029.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.086367 restraints weight = 11029.860| |-----------------------------------------------------------------------------| r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2968 Z= 0.164 Angle : 0.762 15.637 4070 Z= 0.384 Chirality : 0.049 0.148 453 Planarity : 0.006 0.062 531 Dihedral : 6.352 42.717 430 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.87 % Favored : 88.13 % Rotamer: Outliers : 1.11 % Allowed : 22.96 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % 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: -3.79 (0.40), residues: 396 helix: -3.67 (0.55), residues: 33 sheet: -1.83 (0.44), residues: 125 loop : -2.84 (0.40), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 87 TYR 0.010 0.001 TYR E 50 PHE 0.013 0.002 PHE D 82 TRP 0.009 0.001 TRP E 110 HIS 0.004 0.002 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 2965) covalent geometry : angle 0.76105 ( 4064) SS BOND : bond 0.01384 ( 3) SS BOND : angle 1.20808 ( 6) hydrogen bonds : bond 0.03257 ( 90) hydrogen bonds : angle 7.75920 ( 213) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 640.44 seconds wall clock time: 11 minutes 43.19 seconds (703.19 seconds total)