Starting phenix.real_space_refine on Mon Jan 13 16:02:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xrq_38610/01_2025/8xrq_38610.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xrq_38610/01_2025/8xrq_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_38610/01_2025/8xrq_38610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xrq_38610/01_2025/8xrq_38610.map" model { file = "/net/cci-nas-00/data/ceres_data/8xrq_38610/01_2025/8xrq_38610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xrq_38610/01_2025/8xrq_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-5571/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: 4.57, per 1000 atoms: 1.42 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: 0.82 Conformation dependent library (CDL) restraints added in 486.2 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: 0.40 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: 0.96 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: 6.660 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: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.570 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.330 ------------------------------------------------------------------------------- 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 : 0.318 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: 0.1950 time to fit residues: 14.6564 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 : 0.359 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.198613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.185412 restraints weight = 7102.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.188630 restraints weight = 4682.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.191008 restraints weight = 3252.970| |-----------------------------------------------------------------------------| r_work (final): 0.4353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4712 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 : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 458 LYS cc_start: 0.1570 (ttmt) cc_final: 0.1224 (tppt) REVERT: B 45 LEU cc_start: 0.7502 (mt) cc_final: 0.7273 (mm) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.2038 time to fit residues: 14.0432 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 : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 0.0030 chunk 17 optimal weight: 0.7980 chunk 21 optimal weight: 0.9980 chunk 16 optimal weight: 0.0270 chunk 35 optimal weight: 0.0970 chunk 11 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 8 optimal weight: 0.3980 chunk 36 optimal weight: 0.9990 overall best weight: 0.2646 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.192947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.178912 restraints weight = 6749.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.182160 restraints weight = 4540.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.184408 restraints weight = 3232.330| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4916 moved from start: 0.3852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 3301 Z= 0.233 Angle : 0.701 6.986 4492 Z= 0.366 Chirality : 0.047 0.163 476 Planarity : 0.007 0.086 578 Dihedral : 5.353 21.226 452 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.22 % Favored : 88.53 % Rotamer: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % 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: -3.33 (0.38), residues: 401 helix: -3.22 (0.85), residues: 21 sheet: -1.46 (0.58), residues: 93 loop : -2.58 (0.33), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 34 HIS 0.004 0.001 HIS A 505 PHE 0.016 0.002 PHE A 486 TYR 0.014 0.002 TYR C 49 ARG 0.005 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 57 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 451 TYR cc_start: 0.6284 (m-80) cc_final: 0.5984 (m-10) REVERT: B 45 LEU cc_start: 0.7734 (mt) cc_final: 0.7419 (mm) REVERT: C 2 ILE cc_start: 0.7007 (pt) cc_final: 0.6202 (pt) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 0.1866 time to fit residues: 12.7537 Evaluate side-chains 56 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 0.7980 chunk 13 optimal weight: 0.9990 chunk 18 optimal weight: 0.0060 chunk 34 optimal weight: 0.4980 chunk 35 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.3394 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.187532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.173673 restraints weight = 6789.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.176739 restraints weight = 4695.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.179020 restraints weight = 3401.571| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5039 moved from start: 0.5077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 3301 Z= 0.269 Angle : 0.719 7.430 4492 Z= 0.379 Chirality : 0.048 0.242 476 Planarity : 0.007 0.081 578 Dihedral : 5.964 28.642 452 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.71 % Favored : 85.04 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: -3.18 (0.39), residues: 401 helix: -2.74 (0.86), residues: 27 sheet: -1.04 (0.59), residues: 91 loop : -2.61 (0.33), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 34 HIS 0.003 0.001 HIS C 91 PHE 0.030 0.002 PHE A 486 TYR 0.015 0.002 TYR C 49 ARG 0.005 0.001 ARG C 61 *********************** 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 61 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 TRP cc_start: 0.7395 (m100) cc_final: 0.7076 (m100) REVERT: C 61 ARG cc_start: 0.4955 (mtp-110) cc_final: 0.4235 (ptt-90) outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1883 time to fit residues: 13.6682 Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 13 optimal weight: 0.0010 chunk 19 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 11 optimal weight: 0.9980 chunk 0 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.3944 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.185090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.169714 restraints weight = 6795.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.173050 restraints weight = 4607.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.175632 restraints weight = 3328.954| |-----------------------------------------------------------------------------| r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5120 moved from start: 0.5957 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= 0.291 Angle : 0.741 7.886 4492 Z= 0.393 Chirality : 0.049 0.227 476 Planarity : 0.007 0.085 578 Dihedral : 6.456 32.068 452 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 12.26 Ramachandran Plot: Outliers : 0.25 % Allowed : 12.97 % Favored : 86.78 % 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 : 0.26 % 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: -3.27 (0.38), residues: 401 helix: -2.70 (0.94), residues: 27 sheet: -1.25 (0.63), residues: 75 loop : -2.57 (0.31), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B 34 HIS 0.006 0.002 HIS C 91 PHE 0.027 0.003 PHE A 486 TYR 0.011 0.002 TYR A 369 ARG 0.006 0.001 ARG C 61 *********************** 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 69 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 491 PRO cc_start: 0.7464 (Cg_endo) cc_final: 0.7097 (Cg_exo) REVERT: B 34 TRP cc_start: 0.7336 (m100) cc_final: 0.7092 (m100) REVERT: B 45 LEU cc_start: 0.7663 (mt) cc_final: 0.7382 (mm) REVERT: C 56 THR cc_start: 0.8692 (t) cc_final: 0.8406 (p) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.1788 time to fit residues: 14.7715 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 : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 13 optimal weight: 0.7980 chunk 30 optimal weight: 0.0050 chunk 35 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 24 optimal weight: 0.0970 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.4980 chunk 0 optimal weight: 0.9980 chunk 9 optimal weight: 0.0070 chunk 31 optimal weight: 0.0270 chunk 34 optimal weight: 0.0370 overall best weight: 0.0346 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN ** 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 = 0.4311 r_free = 0.4311 target = 0.188882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.173061 restraints weight = 6875.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.176721 restraints weight = 4588.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.179299 restraints weight = 3259.295| |-----------------------------------------------------------------------------| r_work (final): 0.4205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5011 moved from start: 0.6020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.060 3301 Z= 0.156 Angle : 0.626 5.431 4492 Z= 0.318 Chirality : 0.044 0.210 476 Planarity : 0.006 0.082 578 Dihedral : 5.156 22.026 452 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.47 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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: -3.11 (0.38), residues: 401 helix: -2.62 (0.90), residues: 27 sheet: -1.40 (0.51), residues: 98 loop : -2.41 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 112 HIS 0.005 0.001 HIS C 91 PHE 0.011 0.001 PHE A 456 TYR 0.012 0.001 TYR A 508 ARG 0.003 0.000 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 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 489 TYR cc_start: 0.4427 (m-80) cc_final: 0.4023 (m-10) REVERT: B 34 TRP cc_start: 0.7378 (m100) cc_final: 0.7143 (m100) REVERT: B 58 ASN cc_start: 0.6965 (t0) cc_final: 0.6645 (t0) REVERT: C 49 TYR cc_start: 0.6548 (p90) cc_final: 0.6206 (p90) REVERT: C 56 THR cc_start: 0.8689 (t) cc_final: 0.8431 (p) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.2057 time to fit residues: 14.7216 Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 0.0770 chunk 22 optimal weight: 0.3980 chunk 17 optimal weight: 0.4980 chunk 9 optimal weight: 0.0970 chunk 1 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 38 optimal weight: 0.0270 chunk 31 optimal weight: 0.0020 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 0.4980 overall best weight: 0.1202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.187543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.172434 restraints weight = 6679.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.175922 restraints weight = 4476.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.178510 restraints weight = 3185.334| |-----------------------------------------------------------------------------| r_work (final): 0.4202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5022 moved from start: 0.6175 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 : 0.617 5.830 4492 Z= 0.318 Chirality : 0.045 0.203 476 Planarity : 0.006 0.083 578 Dihedral : 5.101 19.789 452 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.25 % Allowed : 10.72 % Favored : 89.03 % 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: -2.99 (0.38), residues: 401 helix: -2.61 (0.90), residues: 27 sheet: -1.25 (0.51), residues: 98 loop : -2.34 (0.34), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.005 0.001 HIS C 91 PHE 0.014 0.001 PHE A 486 TYR 0.017 0.001 TYR A 423 ARG 0.004 0.000 ARG C 54 *********************** 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 60 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 489 TYR cc_start: 0.4385 (m-80) cc_final: 0.3982 (m-10) REVERT: B 34 TRP cc_start: 0.7373 (m100) cc_final: 0.7150 (m100) REVERT: B 45 LEU cc_start: 0.7746 (mt) cc_final: 0.7446 (mm) REVERT: B 58 ASN cc_start: 0.6985 (t0) cc_final: 0.6692 (t0) REVERT: C 49 TYR cc_start: 0.6566 (p90) cc_final: 0.6147 (p90) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1891 time to fit residues: 13.4496 Evaluate side-chains 59 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 0.0040 chunk 38 optimal weight: 0.9980 chunk 18 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 37 optimal weight: 0.0070 chunk 39 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 overall best weight: 0.4410 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.182889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.168592 restraints weight = 6801.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4121 r_free = 0.4121 target = 0.171580 restraints weight = 4703.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4147 r_free = 0.4147 target = 0.173805 restraints weight = 3414.953| |-----------------------------------------------------------------------------| r_work (final): 0.4146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5143 moved from start: 0.6933 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= 0.317 Angle : 0.770 8.469 4492 Z= 0.412 Chirality : 0.050 0.208 476 Planarity : 0.007 0.084 578 Dihedral : 6.697 28.979 452 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.96 % Favored : 83.79 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -3.20 (0.38), residues: 401 helix: -3.16 (0.84), residues: 27 sheet: -1.00 (0.59), residues: 80 loop : -2.55 (0.32), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP C 35 HIS 0.010 0.004 HIS C 91 PHE 0.035 0.003 PHE A 486 TYR 0.044 0.002 TYR A 380 ARG 0.005 0.001 ARG C 61 *********************** 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 : 0.346 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7152 (p-90) cc_final: 0.5844 (p-90) REVERT: A 491 PRO cc_start: 0.7427 (Cg_endo) cc_final: 0.7193 (Cg_exo) REVERT: B 34 TRP cc_start: 0.7348 (m100) cc_final: 0.7140 (m100) REVERT: B 45 LEU cc_start: 0.7699 (mt) cc_final: 0.7375 (mm) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1844 time to fit residues: 14.9479 Evaluate side-chains 67 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 14 optimal weight: 0.2980 chunk 5 optimal weight: 0.0050 chunk 1 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 7 optimal weight: 0.0010 chunk 19 optimal weight: 0.2980 overall best weight: 0.2200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.184506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.169635 restraints weight = 6666.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.173065 restraints weight = 4410.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.175604 restraints weight = 3102.845| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5098 moved from start: 0.7029 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 : 0.666 6.412 4492 Z= 0.348 Chirality : 0.047 0.210 476 Planarity : 0.006 0.084 578 Dihedral : 5.731 23.495 452 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.47 % Favored : 86.28 % 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: -3.05 (0.38), residues: 401 helix: -2.94 (0.83), residues: 27 sheet: -0.88 (0.59), residues: 80 loop : -2.47 (0.33), residues: 294 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 353 HIS 0.007 0.002 HIS C 91 PHE 0.024 0.002 PHE A 486 TYR 0.019 0.001 TYR A 423 ARG 0.005 0.000 ARG A 457 *********************** 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 64 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7167 (p-90) cc_final: 0.6803 (p90) REVERT: B 45 LEU cc_start: 0.7699 (mt) cc_final: 0.7382 (mm) REVERT: B 58 ASN cc_start: 0.6968 (t0) cc_final: 0.6761 (t0) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.1736 time to fit residues: 13.2949 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 : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.0070 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 26 optimal weight: 0.0980 chunk 6 optimal weight: 0.5980 overall best weight: 0.4398 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.182731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.166659 restraints weight = 6588.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.170206 restraints weight = 4412.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.172828 restraints weight = 3136.029| |-----------------------------------------------------------------------------| r_work (final): 0.4128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5184 moved from start: 0.7480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 3301 Z= 0.324 Angle : 0.765 8.211 4492 Z= 0.409 Chirality : 0.050 0.208 476 Planarity : 0.008 0.085 578 Dihedral : 6.626 24.686 452 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.25 % Allowed : 16.46 % Favored : 83.29 % 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: -3.36 (0.37), residues: 401 helix: -3.32 (0.75), residues: 27 sheet: -1.40 (0.61), residues: 73 loop : -2.55 (0.31), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 34 HIS 0.009 0.003 HIS C 91 PHE 0.037 0.003 PHE A 486 TYR 0.013 0.002 TYR A 421 ARG 0.012 0.001 ARG A 457 ********************** 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 66 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 353 TRP cc_start: 0.7191 (p-90) cc_final: 0.6235 (p-90) REVERT: A 452 LEU cc_start: 0.6152 (mt) cc_final: 0.5926 (mt) REVERT: B 34 TRP cc_start: 0.7421 (m100) cc_final: 0.7148 (m100) REVERT: B 45 LEU cc_start: 0.7726 (mt) cc_final: 0.7367 (mm) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.1908 time to fit residues: 15.0657 Evaluate side-chains 62 residues out of total 350 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 5 optimal weight: 0.6980 chunk 8 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.0970 chunk 37 optimal weight: 0.0470 chunk 24 optimal weight: 0.0670 chunk 35 optimal weight: 0.3980 overall best weight: 0.2414 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.184201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.169211 restraints weight = 6695.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.172596 restraints weight = 4488.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.174989 restraints weight = 3186.738| |-----------------------------------------------------------------------------| r_work (final): 0.4153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5130 moved from start: 0.7552 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= 0.219 Angle : 0.683 6.963 4492 Z= 0.357 Chirality : 0.046 0.208 476 Planarity : 0.007 0.085 578 Dihedral : 5.865 20.399 452 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.25 % Allowed : 13.72 % Favored : 86.03 % 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: -3.28 (0.38), residues: 401 helix: -3.01 (0.87), residues: 27 sheet: -1.38 (0.61), residues: 73 loop : -2.51 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 34 HIS 0.007 0.002 HIS C 91 PHE 0.024 0.002 PHE A 486 TYR 0.018 0.001 TYR A 423 ARG 0.005 0.000 ARG C 61 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1863.84 seconds wall clock time: 34 minutes 11.28 seconds (2051.28 seconds total)