Starting phenix.real_space_refine on Fri Dec 27 06:15:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yvm_34132/12_2024/7yvm_34132.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yvm_34132/12_2024/7yvm_34132.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yvm_34132/12_2024/7yvm_34132.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yvm_34132/12_2024/7yvm_34132.map" model { file = "/net/cci-nas-00/data/ceres_data/7yvm_34132/12_2024/7yvm_34132.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yvm_34132/12_2024/7yvm_34132.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.029 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 16 5.16 5 C 1991 2.51 5 N 528 2.21 5 O 591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 3126 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 821 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 101} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 870 Classifications: {'peptide': 118} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 2, 'TRANS': 115} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 1435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1435 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 11, 'TRANS': 181} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 136 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 5, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Time building chain proxies: 5.03, per 1000 atoms: 1.61 Number of scatterers: 3126 At special positions: 0 Unit cell: (62.32, 72.16, 100.04, 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 16 16.00 O 591 8.00 N 528 7.00 C 1991 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 23 " - pdb=" SG CYS A 88 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.06 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.07 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.09 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.04 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: 0.69 Conformation dependent library (CDL) restraints added in 479.3 milliseconds 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 9.5% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 79 through 83 removed outlier: 4.134A pdb=" N SER A 83 " --> pdb=" O SER A 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 75 Processing helix chain 'C' and resid 86 through 90 removed outlier: 4.139A pdb=" N THR C 90 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 344 Processing helix chain 'B' and resid 383 through 390 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.838A pdb=" N SER B 408 " --> pdb=" O ASN B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 3.821A pdb=" N GLU A 70 " --> pdb=" O SER A 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 13 removed outlier: 6.680A pdb=" N LEU A 11 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N VAL A 85 " --> pdb=" O GLN A 38 " (cutoff:3.500A) removed outlier: 5.892A pdb=" N LEU A 33 " --> pdb=" O TYR A 49 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N TYR A 49 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP A 35 " --> pdb=" O LEU A 47 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA4, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.998A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.588A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 10 through 12 removed outlier: 5.998A pdb=" N GLY C 10 " --> pdb=" O THR C 115 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N TYR C 107 " --> pdb=" O ARG C 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.667A pdb=" N ASN B 394 " --> pdb=" O GLU B 516 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N CYS B 432 " --> pdb=" O LEU B 513 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 106 hydrogen bonds defined for protein. 252 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: 0.86 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: 1.17 - 1.31: 505 1.31 - 1.44: 942 1.44 - 1.58: 1737 1.58 - 1.71: 0 1.71 - 1.85: 20 Bond restraints: 3204 Sorted by residual: bond pdb=" C TYR C 33 " pdb=" O TYR C 33 " ideal model delta sigma weight residual 1.235 1.172 0.063 1.26e-02 6.30e+03 2.50e+01 bond pdb=" C PRO A 95 " pdb=" O PRO A 95 " ideal model delta sigma weight residual 1.240 1.186 0.055 1.12e-02 7.97e+03 2.39e+01 bond pdb=" N GLY A 101 " pdb=" CA GLY A 101 " ideal model delta sigma weight residual 1.442 1.479 -0.037 7.70e-03 1.69e+04 2.30e+01 bond pdb=" CA ASN A 93 " pdb=" C ASN A 93 " ideal model delta sigma weight residual 1.523 1.464 0.059 1.28e-02 6.10e+03 2.16e+01 bond pdb=" C THR A 99 " pdb=" O THR A 99 " ideal model delta sigma weight residual 1.235 1.186 0.049 1.13e-02 7.83e+03 1.90e+01 ... (remaining 3199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.04: 4287 4.04 - 8.08: 70 8.08 - 12.12: 8 12.12 - 16.16: 1 16.16 - 20.20: 3 Bond angle restraints: 4369 Sorted by residual: angle pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta sigma weight residual 119.84 138.11 -18.27 1.25e+00 6.40e-01 2.14e+02 angle pdb=" N PRO B 521 " pdb=" CA PRO B 521 " pdb=" C PRO B 521 " ideal model delta sigma weight residual 112.33 92.13 20.20 1.87e+00 2.86e-01 1.17e+02 angle pdb=" C TYR A 98 " pdb=" CA TYR A 98 " pdb=" CB TYR A 98 " ideal model delta sigma weight residual 109.99 93.12 16.87 1.61e+00 3.86e-01 1.10e+02 angle pdb=" C ARG C 97 " pdb=" CA ARG C 97 " pdb=" CB ARG C 97 " ideal model delta sigma weight residual 111.23 99.22 12.01 1.68e+00 3.54e-01 5.11e+01 angle pdb=" C ARG B 454 " pdb=" CA ARG B 454 " pdb=" CB ARG B 454 " ideal model delta sigma weight residual 110.19 99.37 10.82 1.62e+00 3.81e-01 4.46e+01 ... (remaining 4364 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.11: 1776 24.11 - 48.22: 86 48.22 - 72.32: 10 72.32 - 96.43: 0 96.43 - 120.54: 1 Dihedral angle restraints: 1873 sinusoidal: 667 harmonic: 1206 Sorted by residual: dihedral pdb=" CA PRO A 95 " pdb=" C PRO A 95 " pdb=" N PRO A 96 " pdb=" CA PRO A 96 " ideal model delta harmonic sigma weight residual -180.00 -59.46 -120.54 0 5.00e+00 4.00e-02 5.81e+02 dihedral pdb=" C TRP A 94 " pdb=" N TRP A 94 " pdb=" CA TRP A 94 " pdb=" CB TRP A 94 " ideal model delta harmonic sigma weight residual -122.60 -151.47 28.87 0 2.50e+00 1.60e-01 1.33e+02 dihedral pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CA TRP A 94 " pdb=" CB TRP A 94 " ideal model delta harmonic sigma weight residual 122.80 151.58 -28.78 0 2.50e+00 1.60e-01 1.33e+02 ... (remaining 1870 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.252: 476 0.252 - 0.504: 5 0.504 - 0.757: 0 0.757 - 1.009: 0 1.009 - 1.261: 1 Chirality restraints: 482 Sorted by residual: chirality pdb=" CA TRP A 94 " pdb=" N TRP A 94 " pdb=" C TRP A 94 " pdb=" CB TRP A 94 " both_signs ideal model delta sigma weight residual False 2.51 1.25 1.26 2.00e-01 2.50e+01 3.97e+01 chirality pdb=" CA CYS C 95 " pdb=" N CYS C 95 " pdb=" C CYS C 95 " pdb=" CB CYS C 95 " both_signs ideal model delta sigma weight residual False 2.51 2.93 -0.42 2.00e-01 2.50e+01 4.50e+00 chirality pdb=" CA TYR A 98 " pdb=" N TYR A 98 " pdb=" C TYR A 98 " pdb=" CB TYR A 98 " both_signs ideal model delta sigma weight residual False 2.51 2.87 -0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 479 not shown) Planarity restraints: 566 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 90 " -0.036 2.00e-02 2.50e+03 7.38e-02 5.45e+01 pdb=" C GLN A 90 " 0.128 2.00e-02 2.50e+03 pdb=" O GLN A 90 " -0.047 2.00e-02 2.50e+03 pdb=" N TYR A 91 " -0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP A 94 " -0.086 5.00e-02 4.00e+02 1.34e-01 2.87e+01 pdb=" N PRO A 95 " 0.232 5.00e-02 4.00e+02 pdb=" CA PRO A 95 " -0.071 5.00e-02 4.00e+02 pdb=" CD PRO A 95 " -0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 94 " 0.049 2.00e-02 2.50e+03 2.66e-02 1.77e+01 pdb=" CG TRP A 94 " -0.051 2.00e-02 2.50e+03 pdb=" CD1 TRP A 94 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP A 94 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 94 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TRP A 94 " 0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A 94 " -0.039 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 94 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 94 " 0.013 2.00e-02 2.50e+03 pdb=" CH2 TRP A 94 " 0.017 2.00e-02 2.50e+03 ... (remaining 563 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 205 2.71 - 3.26: 3153 3.26 - 3.81: 4790 3.81 - 4.35: 5932 4.35 - 4.90: 9876 Nonbonded interactions: 23956 Sorted by model distance: nonbonded pdb=" OH TYR A 98 " pdb=" OG1 THR C 105 " model vdw 2.166 3.040 nonbonded pdb=" O SER A 77 " pdb=" NE2 GLN A 79 " model vdw 2.275 3.120 nonbonded pdb=" NH1 ARG C 66 " pdb=" O ASN C 83 " model vdw 2.349 3.120 nonbonded pdb=" O LEU B 518 " pdb=" C HIS B 519 " model vdw 2.357 3.270 nonbonded pdb=" SD MET A 4 " pdb=" OE1 GLN A 90 " model vdw 2.363 3.400 ... (remaining 23951 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: 7.430 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.940 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 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 : 0.009 0.063 3204 Z= 0.602 Angle : 1.377 20.197 4369 Z= 0.858 Chirality : 0.092 1.261 482 Planarity : 0.009 0.134 566 Dihedral : 13.483 120.539 1091 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 28.59 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.94 % Favored : 90.58 % Rotamer: Outliers : 1.57 % Allowed : 7.55 % Favored : 90.88 % Cbeta Deviations : 1.57 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.19 (0.34), residues: 414 helix: -4.90 (0.26), residues: 21 sheet: -1.69 (0.41), residues: 127 loop : -3.36 (0.31), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.008 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.034 0.003 PHE B 347 TYR 0.044 0.003 TYR B 380 ARG 0.010 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 102 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8297 (mp) cc_final: 0.7834 (mt) REVERT: C 59 TYR cc_start: 0.8050 (m-80) cc_final: 0.7160 (m-80) REVERT: B 432 CYS cc_start: 0.5883 (p) cc_final: 0.4893 (p) outliers start: 5 outliers final: 3 residues processed: 106 average time/residue: 0.1678 time to fit residues: 21.1432 Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ARG Chi-restraints excluded: chain A residue 95 PRO Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 0.0980 chunk 31 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 11 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 493 GLN B 506 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 3204 Z= 0.251 Angle : 0.758 10.577 4369 Z= 0.391 Chirality : 0.048 0.245 482 Planarity : 0.006 0.083 566 Dihedral : 5.957 54.084 466 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.48 % Allowed : 4.35 % Favored : 95.17 % Rotamer: Outliers : 3.46 % Allowed : 16.04 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.38), residues: 414 helix: -3.55 (0.75), residues: 23 sheet: -1.20 (0.41), residues: 133 loop : -2.12 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP C 47 HIS 0.001 0.000 HIS B 519 PHE 0.017 0.002 PHE B 371 TYR 0.020 0.002 TYR A 49 ARG 0.003 0.001 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 68 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8315 (mp) cc_final: 0.7907 (mt) REVERT: C 34 MET cc_start: 0.8048 (mmm) cc_final: 0.7833 (mmm) REVERT: C 59 TYR cc_start: 0.7892 (m-80) cc_final: 0.7040 (m-80) REVERT: B 418 ILE cc_start: 0.8711 (OUTLIER) cc_final: 0.8445 (mt) REVERT: B 422 ASN cc_start: 0.8670 (OUTLIER) cc_final: 0.8470 (m110) outliers start: 11 outliers final: 5 residues processed: 73 average time/residue: 0.1774 time to fit residues: 15.4396 Evaluate side-chains 66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 59 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 422 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.0270 chunk 24 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 0.2980 chunk 39 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 GLN ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 422 ASN B 493 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7245 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 3204 Z= 0.244 Angle : 0.706 11.041 4369 Z= 0.362 Chirality : 0.047 0.325 482 Planarity : 0.006 0.066 566 Dihedral : 5.149 50.855 458 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.56 % Favored : 94.20 % Rotamer: Outliers : 4.09 % Allowed : 20.75 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.39), residues: 414 helix: -1.84 (1.06), residues: 21 sheet: -0.79 (0.42), residues: 133 loop : -1.75 (0.38), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 47 HIS 0.001 0.000 HIS B 519 PHE 0.030 0.002 PHE B 392 TYR 0.016 0.002 TYR A 49 ARG 0.003 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8404 (mp) cc_final: 0.7985 (mt) REVERT: A 70 GLU cc_start: 0.7242 (mm-30) cc_final: 0.6958 (mp0) REVERT: C 59 TYR cc_start: 0.7854 (m-80) cc_final: 0.7098 (m-80) REVERT: B 418 ILE cc_start: 0.8979 (OUTLIER) cc_final: 0.8663 (mt) REVERT: B 436 TRP cc_start: 0.6558 (OUTLIER) cc_final: 0.5759 (m-10) outliers start: 13 outliers final: 6 residues processed: 74 average time/residue: 0.1732 time to fit residues: 15.1936 Evaluate side-chains 68 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 436 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.1980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 3204 Z= 0.267 Angle : 0.705 8.064 4369 Z= 0.369 Chirality : 0.045 0.222 482 Planarity : 0.006 0.075 566 Dihedral : 5.279 47.368 458 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 6.92 % Allowed : 19.18 % Favored : 73.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.81 (0.40), residues: 414 helix: -2.50 (0.82), residues: 27 sheet: -0.25 (0.44), residues: 129 loop : -1.63 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 94 HIS 0.000 0.000 HIS B 505 PHE 0.020 0.002 PHE B 392 TYR 0.016 0.002 TYR A 49 ARG 0.003 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8510 (mp) cc_final: 0.8027 (mt) REVERT: A 70 GLU cc_start: 0.7316 (mm-30) cc_final: 0.7041 (mp0) REVERT: C 59 TYR cc_start: 0.7864 (m-80) cc_final: 0.7100 (m-80) REVERT: B 351 TYR cc_start: 0.7527 (OUTLIER) cc_final: 0.6873 (t80) REVERT: B 418 ILE cc_start: 0.8953 (OUTLIER) cc_final: 0.8751 (mt) REVERT: B 436 TRP cc_start: 0.6735 (OUTLIER) cc_final: 0.5921 (m-10) outliers start: 22 outliers final: 13 residues processed: 79 average time/residue: 0.1581 time to fit residues: 15.0041 Evaluate side-chains 74 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.0020 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 7.9990 chunk 9 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 3204 Z= 0.261 Angle : 0.723 15.078 4369 Z= 0.373 Chirality : 0.046 0.247 482 Planarity : 0.005 0.066 566 Dihedral : 5.142 47.878 458 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 6.29 % Allowed : 20.75 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.40), residues: 414 helix: -1.49 (1.03), residues: 21 sheet: -0.17 (0.43), residues: 143 loop : -1.65 (0.39), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 353 HIS 0.001 0.000 HIS B 505 PHE 0.038 0.002 PHE B 377 TYR 0.014 0.001 TYR A 49 ARG 0.003 0.001 ARG C 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 65 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8556 (mp) cc_final: 0.8078 (mt) REVERT: C 59 TYR cc_start: 0.7877 (m-80) cc_final: 0.7136 (m-80) REVERT: B 351 TYR cc_start: 0.7576 (OUTLIER) cc_final: 0.6988 (t80) REVERT: B 418 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8759 (mt) REVERT: B 436 TRP cc_start: 0.6726 (OUTLIER) cc_final: 0.5871 (m-10) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.1722 time to fit residues: 15.9944 Evaluate side-chains 72 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3204 Z= 0.256 Angle : 0.721 14.338 4369 Z= 0.371 Chirality : 0.045 0.224 482 Planarity : 0.005 0.065 566 Dihedral : 5.149 46.260 458 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 7.55 % Allowed : 21.70 % Favored : 70.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.40), residues: 414 helix: -1.51 (1.06), residues: 21 sheet: -0.16 (0.44), residues: 142 loop : -1.76 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.020 0.002 PHE B 392 TYR 0.013 0.001 TYR A 49 ARG 0.002 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 58 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8555 (mp) cc_final: 0.8100 (mt) REVERT: A 79 GLN cc_start: 0.7094 (mp10) cc_final: 0.6663 (mp10) REVERT: C 59 TYR cc_start: 0.7894 (m-80) cc_final: 0.7170 (m-80) REVERT: B 351 TYR cc_start: 0.7651 (OUTLIER) cc_final: 0.7058 (t80) REVERT: B 436 TRP cc_start: 0.6748 (OUTLIER) cc_final: 0.6296 (m-10) outliers start: 24 outliers final: 16 residues processed: 76 average time/residue: 0.2025 time to fit residues: 18.1639 Evaluate side-chains 71 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.5149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3204 Z= 0.340 Angle : 0.791 14.240 4369 Z= 0.409 Chirality : 0.046 0.228 482 Planarity : 0.006 0.067 566 Dihedral : 5.589 47.897 458 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.97 % Favored : 92.03 % Rotamer: Outliers : 7.23 % Allowed : 21.38 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.39), residues: 414 helix: -1.65 (0.99), residues: 21 sheet: -0.30 (0.42), residues: 153 loop : -1.99 (0.37), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.033 0.003 PHE B 392 TYR 0.024 0.002 TYR B 380 ARG 0.005 0.001 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.367 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8665 (mp) cc_final: 0.8108 (mt) REVERT: A 79 GLN cc_start: 0.7146 (mp10) cc_final: 0.6667 (mp10) REVERT: C 59 TYR cc_start: 0.8026 (m-80) cc_final: 0.7227 (m-80) REVERT: B 351 TYR cc_start: 0.7807 (OUTLIER) cc_final: 0.7205 (t80) REVERT: B 374 PHE cc_start: 0.4442 (m-10) cc_final: 0.4194 (m-10) REVERT: B 436 TRP cc_start: 0.7036 (OUTLIER) cc_final: 0.6505 (m-10) outliers start: 23 outliers final: 18 residues processed: 71 average time/residue: 0.1754 time to fit residues: 14.6896 Evaluate side-chains 71 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 57 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 68 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Chi-restraints excluded: chain B residue 503 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 35 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 21 optimal weight: 4.9990 chunk 15 optimal weight: 0.2980 chunk 28 optimal weight: 0.0670 chunk 11 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 23 optimal weight: 0.2980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7326 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3204 Z= 0.216 Angle : 0.723 13.522 4369 Z= 0.370 Chirality : 0.044 0.217 482 Planarity : 0.005 0.057 566 Dihedral : 5.030 43.705 458 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.00 % Favored : 93.00 % Rotamer: Outliers : 5.66 % Allowed : 23.90 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.40), residues: 414 helix: -1.28 (1.04), residues: 21 sheet: -0.10 (0.44), residues: 142 loop : -1.95 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.001 0.000 HIS B 505 PHE 0.020 0.002 PHE B 392 TYR 0.014 0.001 TYR B 380 ARG 0.010 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8595 (mp) cc_final: 0.8172 (mt) REVERT: A 79 GLN cc_start: 0.7088 (mp10) cc_final: 0.6711 (mp10) REVERT: C 59 TYR cc_start: 0.7941 (m-80) cc_final: 0.7207 (m-80) REVERT: B 351 TYR cc_start: 0.7522 (OUTLIER) cc_final: 0.6975 (t80) REVERT: B 356 LYS cc_start: 0.7893 (ptmt) cc_final: 0.7470 (mmmm) REVERT: B 374 PHE cc_start: 0.4101 (m-10) cc_final: 0.3841 (m-10) REVERT: B 436 TRP cc_start: 0.6752 (OUTLIER) cc_final: 0.5852 (m-10) outliers start: 18 outliers final: 15 residues processed: 74 average time/residue: 0.1733 time to fit residues: 15.4020 Evaluate side-chains 73 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 56 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 92 ASN Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.5490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3204 Z= 0.275 Angle : 0.754 13.272 4369 Z= 0.386 Chirality : 0.045 0.224 482 Planarity : 0.005 0.064 566 Dihedral : 5.202 44.025 458 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Rotamer: Outliers : 5.66 % Allowed : 25.16 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.39), residues: 414 helix: -1.41 (0.97), residues: 21 sheet: -0.14 (0.43), residues: 143 loop : -1.96 (0.37), residues: 250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 47 HIS 0.001 0.001 HIS B 505 PHE 0.014 0.002 PHE C 67 TYR 0.016 0.001 TYR B 380 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.364 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8617 (mp) cc_final: 0.8171 (mt) REVERT: A 79 GLN cc_start: 0.7142 (mp10) cc_final: 0.6724 (mp10) REVERT: C 59 TYR cc_start: 0.7991 (m-80) cc_final: 0.7253 (m-80) REVERT: B 351 TYR cc_start: 0.7582 (OUTLIER) cc_final: 0.7082 (t80) REVERT: B 436 TRP cc_start: 0.6769 (OUTLIER) cc_final: 0.6505 (m-10) outliers start: 18 outliers final: 16 residues processed: 66 average time/residue: 0.1690 time to fit residues: 13.4219 Evaluate side-chains 68 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 391 CYS Chi-restraints excluded: chain B residue 393 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 436 TRP Chi-restraints excluded: chain B residue 438 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.5980 chunk 9 optimal weight: 0.0030 chunk 29 optimal weight: 0.5980 chunk 4 optimal weight: 0.0770 chunk 8 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 overall best weight: 0.4148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 moved from start: 0.5682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 3204 Z= 0.218 Angle : 0.716 13.003 4369 Z= 0.368 Chirality : 0.044 0.213 482 Planarity : 0.005 0.054 566 Dihedral : 4.908 41.857 458 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 4.40 % Allowed : 25.16 % Favored : 70.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.62 (0.41), residues: 414 helix: -0.33 (1.29), residues: 15 sheet: -0.18 (0.43), residues: 144 loop : -1.74 (0.39), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.001 0.001 HIS B 505 PHE 0.017 0.002 PHE B 374 TYR 0.014 0.001 TYR B 380 ARG 0.003 0.000 ARG C 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 828 Ramachandran restraints generated. 414 Oldfield, 0 Emsley, 414 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.374 Fit side-chains revert: symmetry clash REVERT: A 2 ILE cc_start: 0.8560 (mp) cc_final: 0.8116 (mt) REVERT: A 11 LEU cc_start: 0.7966 (mt) cc_final: 0.7692 (mp) REVERT: C 59 TYR cc_start: 0.7967 (m-80) cc_final: 0.7227 (m-80) REVERT: B 351 TYR cc_start: 0.7388 (OUTLIER) cc_final: 0.6907 (t80) REVERT: B 356 LYS cc_start: 0.7855 (ptmt) cc_final: 0.7472 (mmtp) outliers start: 14 outliers final: 11 residues processed: 69 average time/residue: 0.1838 time to fit residues: 15.1966 Evaluate side-chains 71 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 70 GLU Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 99 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 90 THR Chi-restraints excluded: chain B residue 351 TYR Chi-restraints excluded: chain B residue 371 PHE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 434 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 ASN ** C 3 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 = 0.3952 r_free = 0.3952 target = 0.144092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.126624 restraints weight = 6590.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.129515 restraints weight = 3875.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.131439 restraints weight = 2687.417| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.5748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 3204 Z= 0.290 Angle : 0.773 12.902 4369 Z= 0.396 Chirality : 0.046 0.221 482 Planarity : 0.005 0.063 566 Dihedral : 5.163 42.707 458 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 6.29 % Allowed : 24.53 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 5.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.40), residues: 414 helix: -0.89 (1.05), residues: 21 sheet: -0.27 (0.42), residues: 152 loop : -1.91 (0.39), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 436 HIS 0.001 0.000 HIS B 505 PHE 0.033 0.002 PHE B 374 TYR 0.016 0.001 TYR B 380 ARG 0.003 0.000 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1502.95 seconds wall clock time: 27 minutes 40.91 seconds (1660.91 seconds total)