Starting phenix.real_space_refine on Fri Dec 27 06:29:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrq_38610/12_2024/8xrq_38610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrq_38610/12_2024/8xrq_38610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xrq_38610/12_2024/8xrq_38610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrq_38610/12_2024/8xrq_38610.map" model { file = "/net/cci-nas-00/data/ceres_data/8xrq_38610/12_2024/8xrq_38610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrq_38610/12_2024/8xrq_38610.cif" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 11 5.16 5 C 2053 2.51 5 N 537 2.21 5 O 609 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3210 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1462 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Chain: "B" Number of atoms: 934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 934 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 5, 'TRANS': 115} Chain: "C" Number of atoms: 814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 814 Classifications: {'peptide': 106} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 98} Time building chain proxies: 5.28, per 1000 atoms: 1.64 Number of scatterers: 3210 At special positions: 0 Unit cell: (71.048, 84.744, 68.48, 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 11 16.00 O 609 8.00 N 537 7.00 C 2053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.04 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.69 Conformation dependent library (CDL) restraints added in 355.5 milliseconds 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 746 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 8 sheets defined 4.9% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'A' and resid 365 through 371 removed outlier: 3.566A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 411 removed outlier: 5.067A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 421 removed outlier: 3.524A pdb=" N TYR A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.704A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 357 through 358 removed outlier: 3.704A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 57 through 59 removed outlier: 3.877A pdb=" N ASN B 58 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N TYR B 50 " --> pdb=" O ASN B 58 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N TRP B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N ARG B 38 " --> pdb=" O TRP B 47 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLY B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP B 34 " --> pdb=" O VAL B 51 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN B 39 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N VAL B 92 " --> pdb=" O GLN B 39 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N CYS B 95 " --> pdb=" O TRP B 112 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TRP B 112 " --> pdb=" O CYS B 95 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ARG B 97 " --> pdb=" O ASP B 110 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'C' and resid 19 through 21 removed outlier: 4.247A pdb=" N ILE C 75 " --> pdb=" O ALA C 19 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N LEU C 21 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU C 73 " --> pdb=" O LEU C 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.687A pdb=" N ASN C 53 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N TYR C 49 " --> pdb=" O LEU C 33 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU C 33 " --> pdb=" O TYR C 49 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN C 38 " --> pdb=" O VAL C 85 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL C 85 " --> pdb=" O GLN C 38 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 105 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: 0.73 Time building geometry restraints manager: 0.82 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: 984 1.34 - 1.46: 813 1.46 - 1.58: 1490 1.58 - 1.70: 2 1.70 - 1.82: 12 Bond restraints: 3301 Sorted by residual: bond pdb=" C PHE B 78 " pdb=" N SER B 79 " ideal model delta sigma weight residual 1.331 1.440 -0.110 1.41e-02 5.03e+03 6.06e+01 bond pdb=" C ILE B 29 " pdb=" N SER B 30 " ideal model delta sigma weight residual 1.332 1.419 -0.087 1.38e-02 5.25e+03 3.96e+01 bond pdb=" C MET B 117 " pdb=" N VAL B 118 " ideal model delta sigma weight residual 1.330 1.403 -0.073 1.21e-02 6.83e+03 3.67e+01 bond pdb=" C VAL B 118 " pdb=" N THR B 119 " ideal model delta sigma weight residual 1.331 1.260 0.071 1.23e-02 6.61e+03 3.32e+01 bond pdb=" C SER B 40 " pdb=" N PRO B 41 " ideal model delta sigma weight residual 1.331 1.388 -0.057 1.21e-02 6.83e+03 2.21e+01 ... (remaining 3296 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 4337 2.08 - 4.16: 119 4.16 - 6.24: 27 6.24 - 8.32: 7 8.32 - 10.40: 2 Bond angle restraints: 4492 Sorted by residual: angle pdb=" C SER B 40 " pdb=" N PRO B 41 " pdb=" CA PRO B 41 " ideal model delta sigma weight residual 120.11 110.63 9.48 1.12e+00 7.97e-01 7.16e+01 angle pdb=" N SER B 62 " pdb=" CA SER B 62 " pdb=" C SER B 62 " ideal model delta sigma weight residual 111.14 104.25 6.89 1.08e+00 8.57e-01 4.07e+01 angle pdb=" CA PRO C 40 " pdb=" N PRO C 40 " pdb=" CD PRO C 40 " ideal model delta sigma weight residual 112.00 103.92 8.08 1.40e+00 5.10e-01 3.33e+01 angle pdb=" O PHE B 78 " pdb=" C PHE B 78 " pdb=" N SER B 79 " ideal model delta sigma weight residual 123.06 129.73 -6.67 1.20e+00 6.94e-01 3.09e+01 angle pdb=" CA PHE B 78 " pdb=" C PHE B 78 " pdb=" N SER B 79 " ideal model delta sigma weight residual 115.91 108.96 6.95 1.29e+00 6.01e-01 2.90e+01 ... (remaining 4487 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 1674 18.00 - 36.00: 197 36.00 - 54.00: 43 54.00 - 72.00: 6 72.00 - 89.99: 4 Dihedral angle restraints: 1924 sinusoidal: 746 harmonic: 1178 Sorted by residual: dihedral pdb=" CB CYS B 22 " pdb=" SG CYS B 22 " pdb=" SG CYS B 95 " pdb=" CB CYS B 95 " ideal model delta sinusoidal sigma weight residual 93.00 157.56 -64.56 1 1.00e+01 1.00e-02 5.48e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual -86.00 -135.81 49.81 1 1.00e+01 1.00e-02 3.40e+01 dihedral pdb=" CA ASP B 89 " pdb=" CB ASP B 89 " pdb=" CG ASP B 89 " pdb=" OD1 ASP B 89 " ideal model delta sinusoidal sigma weight residual -30.00 -89.16 59.16 1 2.00e+01 2.50e-03 1.17e+01 ... (remaining 1921 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 299 0.038 - 0.075: 121 0.075 - 0.113: 45 0.113 - 0.151: 9 0.151 - 0.188: 2 Chirality restraints: 476 Sorted by residual: chirality pdb=" CA VAL B 118 " pdb=" N VAL B 118 " pdb=" C VAL B 118 " pdb=" CB VAL B 118 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 8.86e-01 chirality pdb=" CA VAL A 511 " pdb=" N VAL A 511 " pdb=" C VAL A 511 " pdb=" CB VAL A 511 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 6.83e-01 chirality pdb=" CA VAL C 104 " pdb=" N VAL C 104 " pdb=" C VAL C 104 " pdb=" CB VAL C 104 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 473 not shown) Planarity restraints: 578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 40 " 0.024 2.00e-02 2.50e+03 4.73e-02 2.24e+01 pdb=" C SER B 40 " -0.082 2.00e-02 2.50e+03 pdb=" O SER B 40 " 0.031 2.00e-02 2.50e+03 pdb=" N PRO B 41 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS C 39 " 0.068 5.00e-02 4.00e+02 9.81e-02 1.54e+01 pdb=" N PRO C 40 " -0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 40 " 0.048 5.00e-02 4.00e+02 pdb=" CD PRO C 40 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 29 " -0.018 2.00e-02 2.50e+03 3.75e-02 1.41e+01 pdb=" C ILE B 29 " 0.065 2.00e-02 2.50e+03 pdb=" O ILE B 29 " -0.026 2.00e-02 2.50e+03 pdb=" N SER B 30 " -0.021 2.00e-02 2.50e+03 ... (remaining 575 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 1157 2.84 - 3.35: 2737 3.35 - 3.87: 4951 3.87 - 4.38: 5461 4.38 - 4.90: 9458 Nonbonded interactions: 23764 Sorted by model distance: nonbonded pdb=" O THR A 430 " pdb=" OG1 THR A 430 " model vdw 2.322 3.040 nonbonded pdb=" OE1 GLN C 42 " pdb=" O ALA C 43 " model vdw 2.417 3.040 nonbonded pdb=" O SER A 438 " pdb=" OG SER A 438 " model vdw 2.442 3.040 nonbonded pdb=" O SER B 103 " pdb=" N TRP B 105 " model vdw 2.463 3.120 nonbonded pdb=" O SER A 496 " pdb=" OG SER A 496 " model vdw 2.463 3.040 ... (remaining 23759 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: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.860 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4714 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.110 3301 Z= 0.443 Angle : 0.867 10.399 4492 Z= 0.541 Chirality : 0.047 0.188 476 Planarity : 0.008 0.098 578 Dihedral : 15.749 89.994 1166 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.97 % Favored : 88.78 % Rotamer: Outliers : 0.86 % Allowed : 22.86 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.50 (0.38), residues: 401 helix: -4.96 (0.50), residues: 6 sheet: -1.66 (0.62), residues: 78 loop : -2.69 (0.31), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 35 HIS 0.001 0.001 HIS B 77 PHE 0.018 0.001 PHE C 83 TYR 0.008 0.001 TYR B 32 ARG 0.004 0.000 ARG B 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 61 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 489 TYR cc_start: 0.5626 (m-80) cc_final: 0.5294 (m-80) REVERT: B 5 GLN cc_start: 0.6697 (mp10) cc_final: 0.6452 (mp10) REVERT: B 36 TRP cc_start: 0.5921 (m100) cc_final: 0.5620 (m100) outliers start: 3 outliers final: 0 residues processed: 64 average time/residue: 0.2060 time to fit residues: 15.4017 Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.0770 chunk 12 optimal weight: 0.0010 chunk 19 optimal weight: 0.3980 chunk 23 optimal weight: 0.0970 chunk 36 optimal weight: 0.2980 chunk 11 optimal weight: 0.0980 overall best weight: 0.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4720 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3301 Z= 0.193 Angle : 0.676 11.483 4492 Z= 0.342 Chirality : 0.047 0.239 476 Planarity : 0.006 0.075 578 Dihedral : 4.803 21.550 452 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.22 % Favored : 87.53 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.45 (0.39), residues: 401 helix: -3.26 (0.92), residues: 21 sheet: -1.70 (0.56), residues: 97 loop : -2.61 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 112 HIS 0.002 0.001 HIS C 91 PHE 0.013 0.002 PHE B 78 TYR 0.028 0.002 TYR B 52 ARG 0.005 0.001 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.1730 (ttmt) cc_final: 0.1417 (tppt) REVERT: B 45 LEU cc_start: 0.7571 (mt) cc_final: 0.7328 (mm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1949 time to fit residues: 13.4339 Evaluate side-chains 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.0070 chunk 10 optimal weight: 0.8980 chunk 36 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.3980 chunk 29 optimal weight: 0.2980 chunk 35 optimal weight: 0.1980 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 0.0010 overall best weight: 0.1804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4824 moved from start: 0.3426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 3301 Z= 0.199 Angle : 0.640 6.469 4492 Z= 0.331 Chirality : 0.045 0.152 476 Planarity : 0.006 0.085 578 Dihedral : 4.864 16.157 452 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.47 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.29 (0.39), residues: 401 helix: -3.21 (0.87), residues: 21 sheet: -1.61 (0.56), residues: 97 loop : -2.48 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 34 HIS 0.002 0.001 HIS A 505 PHE 0.012 0.002 PHE C 71 TYR 0.013 0.001 TYR B 52 ARG 0.003 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.2265 (ttmt) cc_final: 0.1975 (tppt) REVERT: B 45 LEU cc_start: 0.7742 (mt) cc_final: 0.7388 (mm) REVERT: C 3 VAL cc_start: 0.6778 (p) cc_final: 0.6295 (p) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1972 time to fit residues: 14.0894 Evaluate side-chains 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 24 optimal weight: 0.0570 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.0970 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.0980 chunk 10 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 overall best weight: 0.2096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4886 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 3301 Z= 0.199 Angle : 0.629 7.074 4492 Z= 0.328 Chirality : 0.045 0.171 476 Planarity : 0.006 0.086 578 Dihedral : 5.058 21.612 452 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.97 % Favored : 86.78 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.28 (0.39), residues: 401 helix: -3.38 (0.77), residues: 21 sheet: -1.60 (0.51), residues: 111 loop : -2.48 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 34 HIS 0.001 0.001 HIS A 505 PHE 0.016 0.002 PHE A 486 TYR 0.019 0.001 TYR C 49 ARG 0.003 0.000 ARG A 403 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.6126 (m-80) cc_final: 0.5886 (m-10) REVERT: C 56 THR cc_start: 0.8734 (t) cc_final: 0.8366 (p) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1898 time to fit residues: 12.6539 Evaluate side-chains 54 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.0010 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 0.0670 chunk 0 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 7 optimal weight: 0.0570 chunk 22 optimal weight: 0.0020 overall best weight: 0.1450 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4883 moved from start: 0.4769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3301 Z= 0.163 Angle : 0.587 5.865 4492 Z= 0.300 Chirality : 0.044 0.184 476 Planarity : 0.006 0.083 578 Dihedral : 4.738 17.646 452 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.47 % Favored : 88.28 % Rotamer: Outliers : 0.29 % Allowed : 2.57 % Favored : 97.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.00 (0.39), residues: 401 helix: -2.51 (0.90), residues: 27 sheet: -1.06 (0.56), residues: 93 loop : -2.44 (0.34), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 34 HIS 0.001 0.001 HIS C 91 PHE 0.012 0.001 PHE A 486 TYR 0.008 0.001 TYR A 369 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.6145 (m-80) cc_final: 0.5874 (m-80) REVERT: A 489 TYR cc_start: 0.5456 (m-80) cc_final: 0.5068 (m-80) REVERT: C 56 THR cc_start: 0.8701 (t) cc_final: 0.8390 (p) outliers start: 1 outliers final: 0 residues processed: 56 average time/residue: 0.1866 time to fit residues: 12.5568 Evaluate side-chains 55 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.0870 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 0.0270 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5048 moved from start: 0.6070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 3301 Z= 0.354 Angle : 0.784 7.479 4492 Z= 0.418 Chirality : 0.051 0.323 476 Planarity : 0.008 0.085 578 Dihedral : 6.584 27.816 452 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.71 % Favored : 84.29 % Rotamer: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.23 (0.39), residues: 401 helix: -2.93 (0.91), residues: 27 sheet: -1.18 (0.66), residues: 73 loop : -2.52 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP C 35 HIS 0.008 0.002 HIS C 91 PHE 0.037 0.003 PHE A 486 TYR 0.017 0.002 TYR C 49 ARG 0.005 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 448 ASN cc_start: 0.7941 (t0) cc_final: 0.7679 (t0) REVERT: A 491 PRO cc_start: 0.7204 (Cg_endo) cc_final: 0.6800 (Cg_exo) REVERT: B 45 LEU cc_start: 0.7822 (mt) cc_final: 0.7457 (mm) REVERT: C 56 THR cc_start: 0.8723 (t) cc_final: 0.8441 (p) REVERT: C 61 ARG cc_start: 0.5252 (mtp-110) cc_final: 0.4514 (ptt90) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1973 time to fit residues: 16.0735 Evaluate side-chains 65 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 0.0970 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.0980 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 11 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.4980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5031 moved from start: 0.6391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 3301 Z= 0.263 Angle : 0.709 6.528 4492 Z= 0.374 Chirality : 0.047 0.171 476 Planarity : 0.006 0.084 578 Dihedral : 6.042 22.741 452 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.72 % Favored : 86.03 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.26 (0.38), residues: 401 helix: -2.91 (0.91), residues: 27 sheet: -1.33 (0.54), residues: 91 loop : -2.55 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 112 HIS 0.006 0.002 HIS C 91 PHE 0.030 0.003 PHE A 486 TYR 0.016 0.002 TYR A 508 ARG 0.006 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 448 ASN cc_start: 0.7916 (t0) cc_final: 0.7709 (t0) REVERT: A 491 PRO cc_start: 0.7140 (Cg_endo) cc_final: 0.6813 (Cg_exo) REVERT: B 45 LEU cc_start: 0.7728 (mt) cc_final: 0.7472 (mt) REVERT: C 56 THR cc_start: 0.8677 (t) cc_final: 0.8395 (p) REVERT: C 61 ARG cc_start: 0.5194 (mtp-110) cc_final: 0.4499 (ptt90) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2009 time to fit residues: 15.6173 Evaluate side-chains 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.0970 chunk 28 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 23 optimal weight: 0.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5115 moved from start: 0.7189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 3301 Z= 0.349 Angle : 0.808 7.471 4492 Z= 0.434 Chirality : 0.052 0.276 476 Planarity : 0.008 0.084 578 Dihedral : 7.032 27.213 452 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.96 % Favored : 82.79 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.74 (0.36), residues: 401 helix: -3.88 (0.75), residues: 25 sheet: -1.47 (0.57), residues: 81 loop : -2.89 (0.30), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP C 35 HIS 0.010 0.003 HIS C 91 PHE 0.042 0.003 PHE A 486 TYR 0.024 0.002 TYR A 423 ARG 0.005 0.001 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7107 (p-90) cc_final: 0.5371 (p-90) REVERT: A 355 ARG cc_start: 0.6607 (tpp80) cc_final: 0.5527 (tpp80) REVERT: A 491 PRO cc_start: 0.7182 (Cg_endo) cc_final: 0.6970 (Cg_exo) REVERT: B 45 LEU cc_start: 0.7768 (mt) cc_final: 0.7521 (mt) REVERT: C 56 THR cc_start: 0.8708 (t) cc_final: 0.8470 (p) REVERT: C 61 ARG cc_start: 0.5353 (mtp-110) cc_final: 0.4653 (ptt90) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1925 time to fit residues: 15.5779 Evaluate side-chains 66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.0670 chunk 23 optimal weight: 0.8980 chunk 18 optimal weight: 0.0040 chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 31 optimal weight: 0.3980 chunk 3 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.2980 chunk 25 optimal weight: 0.4980 overall best weight: 0.2330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5071 moved from start: 0.7216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 3301 Z= 0.221 Angle : 0.696 6.838 4492 Z= 0.365 Chirality : 0.047 0.238 476 Planarity : 0.006 0.086 578 Dihedral : 6.019 21.952 452 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.47 % Favored : 86.28 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.59 (0.38), residues: 401 helix: -3.62 (0.76), residues: 27 sheet: -1.68 (0.50), residues: 105 loop : -2.71 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 353 HIS 0.007 0.002 HIS C 91 PHE 0.027 0.002 PHE A 486 TYR 0.010 0.001 TYR A 369 ARG 0.004 0.001 ARG C 61 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7109 (p-90) cc_final: 0.5845 (p-90) REVERT: A 491 PRO cc_start: 0.7160 (Cg_endo) cc_final: 0.6917 (Cg_exo) REVERT: B 45 LEU cc_start: 0.7688 (mt) cc_final: 0.7455 (mt) REVERT: C 56 THR cc_start: 0.8641 (t) cc_final: 0.8405 (p) REVERT: C 61 ARG cc_start: 0.5208 (mtp-110) cc_final: 0.4559 (ptt90) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1786 time to fit residues: 12.8163 Evaluate side-chains 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 0.3980 chunk 8 optimal weight: 0.2980 chunk 31 optimal weight: 0.0980 chunk 13 optimal weight: 0.2980 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5117 moved from start: 0.7501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 3301 Z= 0.296 Angle : 0.762 6.579 4492 Z= 0.401 Chirality : 0.049 0.213 476 Planarity : 0.007 0.088 578 Dihedral : 6.542 21.958 452 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.71 % Favored : 84.04 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.81 (0.36), residues: 401 helix: -3.89 (0.72), residues: 25 sheet: -1.70 (0.54), residues: 86 loop : -2.89 (0.31), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 35 HIS 0.009 0.003 HIS C 91 PHE 0.035 0.003 PHE A 486 TYR 0.025 0.002 TYR A 423 ARG 0.004 0.001 ARG C 61 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 802 Ramachandran restraints generated. 401 Oldfield, 0 Emsley, 401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7094 (p-90) cc_final: 0.6107 (p-90) REVERT: A 491 PRO cc_start: 0.7131 (Cg_endo) cc_final: 0.6924 (Cg_exo) REVERT: B 45 LEU cc_start: 0.7683 (mt) cc_final: 0.7432 (mt) REVERT: C 56 THR cc_start: 0.8711 (t) cc_final: 0.8485 (p) REVERT: C 61 ARG cc_start: 0.5310 (mtp-110) cc_final: 0.4608 (ptt90) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2020 time to fit residues: 15.5115 Evaluate side-chains 63 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.0060 chunk 36 optimal weight: 0.3980 chunk 21 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.3980 chunk 15 optimal weight: 0.0020 chunk 14 optimal weight: 0.0870 chunk 39 optimal weight: 0.7980 overall best weight: 0.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 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 = 0.4254 r_free = 0.4254 target = 0.183475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.169434 restraints weight = 6771.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.172292 restraints weight = 4715.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.174562 restraints weight = 3456.267| |-----------------------------------------------------------------------------| r_work (final): 0.4149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5133 moved from start: 0.7493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 3301 Z= 0.194 Angle : 0.654 5.843 4492 Z= 0.342 Chirality : 0.045 0.212 476 Planarity : 0.006 0.086 578 Dihedral : 5.710 21.844 452 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.72 % Favored : 86.03 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -3.50 (0.39), residues: 401 helix: -3.53 (0.77), residues: 27 sheet: -1.50 (0.51), residues: 106 loop : -2.71 (0.35), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 353 HIS 0.007 0.003 HIS C 91 PHE 0.019 0.002 PHE A 486 TYR 0.009 0.001 TYR A 369 ARG 0.004 0.001 ARG A 457 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1636.72 seconds wall clock time: 30 minutes 44.99 seconds (1844.99 seconds total)