Starting phenix.real_space_refine on Mon Sep 23 14:08:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/09_2024/8bdz_15995.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/09_2024/8bdz_15995.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/09_2024/8bdz_15995.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/09_2024/8bdz_15995.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/09_2024/8bdz_15995.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8bdz_15995/09_2024/8bdz_15995.cif" } resolution = 3.13 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= 0.063 sd= 0.372 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 18 5.16 5 C 2157 2.51 5 N 546 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 3309 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "B" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Chain: "C" Number of atoms: 1103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1103 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 11, 'TRANS': 126} Chain breaks: 1 Time building chain proxies: 3.84, per 1000 atoms: 1.16 Number of scatterers: 3309 At special positions: 0 Unit cell: (87.4532, 76.3832, 91.8812, 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 18 16.00 O 588 8.00 N 546 7.00 C 2157 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 59 " - pdb=" SG CYS B 59 " 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: 0.79 Conformation dependent library (CDL) restraints added in 435.6 milliseconds 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 0 sheets defined 82.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.600A pdb=" N GLY A 8 " --> pdb=" O LYS A 5 " (cutoff:3.500A) Processing helix chain 'A' and resid 10 through 15 Processing helix chain 'A' and resid 16 through 17 No H-bonds generated for 'chain 'A' and resid 16 through 17' Processing helix chain 'A' and resid 18 through 22 removed outlier: 3.724A pdb=" N PHE A 22 " --> pdb=" O SER A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 24 through 41 removed outlier: 3.911A pdb=" N ARG A 37 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.987A pdb=" N GLU A 38 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N ALA A 39 " --> pdb=" O LEU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 73 removed outlier: 3.604A pdb=" N THR A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 232 removed outlier: 3.918A pdb=" N ASN A 230 " --> pdb=" O VAL A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 251 Processing helix chain 'A' and resid 251 through 268 Processing helix chain 'B' and resid 4 through 8 Processing helix chain 'B' and resid 10 through 16 removed outlier: 3.606A pdb=" N PHE B 16 " --> pdb=" O GLU B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 17 through 22 removed outlier: 6.296A pdb=" N ASP B 20 " --> pdb=" O LEU B 17 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE B 22 " --> pdb=" O SER B 19 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 41 removed outlier: 3.784A pdb=" N ARG B 37 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA B 39 " --> pdb=" O LEU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 47 through 72 removed outlier: 3.530A pdb=" N THR B 51 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 removed outlier: 3.837A pdb=" N VAL B 226 " --> pdb=" O ARG B 222 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 227 " --> pdb=" O ASP B 223 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ASN B 230 " --> pdb=" O VAL B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 251 Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 269 through 273 Processing helix chain 'C' and resid 4 through 8 Processing helix chain 'C' and resid 10 through 16 removed outlier: 3.891A pdb=" N PHE C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 22 removed outlier: 6.033A pdb=" N ASP C 20 " --> pdb=" O LEU C 17 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 42 removed outlier: 3.875A pdb=" N ARG C 37 " --> pdb=" O SER C 33 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU C 38 " --> pdb=" O ALA C 34 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N ALA C 39 " --> pdb=" O LEU C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 47 through 73 Processing helix chain 'C' and resid 222 through 230 removed outlier: 4.111A pdb=" N VAL C 226 " --> pdb=" O ARG C 222 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER C 227 " --> pdb=" O ASP C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 251 removed outlier: 3.789A pdb=" N LYS C 236 " --> pdb=" O ASN C 232 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 268 Processing helix chain 'C' and resid 269 through 273 218 hydrogen bonds defined for protein. 618 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: 1.06 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1032 1.35 - 1.46: 865 1.46 - 1.58: 1487 1.58 - 1.70: 0 1.70 - 1.81: 27 Bond restraints: 3411 Sorted by residual: bond pdb=" CD GLU A 257 " pdb=" OE1 GLU A 257 " ideal model delta sigma weight residual 1.249 1.232 0.017 1.90e-02 2.77e+03 8.33e-01 bond pdb=" CD GLU C 257 " pdb=" OE1 GLU C 257 " ideal model delta sigma weight residual 1.249 1.233 0.016 1.90e-02 2.77e+03 7.43e-01 bond pdb=" CD GLU B 257 " pdb=" OE1 GLU B 257 " ideal model delta sigma weight residual 1.249 1.234 0.015 1.90e-02 2.77e+03 6.64e-01 bond pdb=" CA CYS B 46 " pdb=" CB CYS B 46 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.91e-01 bond pdb=" CB GLU A 257 " pdb=" CG GLU A 257 " ideal model delta sigma weight residual 1.520 1.542 -0.022 3.00e-02 1.11e+03 5.34e-01 ... (remaining 3406 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.27: 4520 1.27 - 2.55: 103 2.55 - 3.82: 32 3.82 - 5.10: 6 5.10 - 6.37: 1 Bond angle restraints: 4662 Sorted by residual: angle pdb=" C HIS B 45 " pdb=" N CYS B 46 " pdb=" CA CYS B 46 " ideal model delta sigma weight residual 121.54 127.91 -6.37 1.91e+00 2.74e-01 1.11e+01 angle pdb=" N GLU A 257 " pdb=" CA GLU A 257 " pdb=" CB GLU A 257 " ideal model delta sigma weight residual 110.39 114.79 -4.40 1.66e+00 3.63e-01 7.02e+00 angle pdb=" C HIS C 45 " pdb=" N CYS C 46 " pdb=" CA CYS C 46 " ideal model delta sigma weight residual 121.54 126.54 -5.00 1.91e+00 2.74e-01 6.86e+00 angle pdb=" N GLU B 257 " pdb=" CA GLU B 257 " pdb=" CB GLU B 257 " ideal model delta sigma weight residual 110.28 114.08 -3.80 1.55e+00 4.16e-01 6.00e+00 angle pdb=" C ILE A 256 " pdb=" N GLU A 257 " pdb=" CA GLU A 257 " ideal model delta sigma weight residual 120.72 116.80 3.92 1.67e+00 3.59e-01 5.51e+00 ... (remaining 4657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.27: 1722 12.27 - 24.53: 194 24.53 - 36.80: 61 36.80 - 49.06: 18 49.06 - 61.32: 6 Dihedral angle restraints: 2001 sinusoidal: 792 harmonic: 1209 Sorted by residual: dihedral pdb=" CA ASP A 2 " pdb=" CB ASP A 2 " pdb=" CG ASP A 2 " pdb=" OD1 ASP A 2 " ideal model delta sinusoidal sigma weight residual -30.00 -87.40 57.40 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CB CYS A 59 " pdb=" SG CYS A 59 " pdb=" SG CYS B 59 " pdb=" CB CYS B 59 " ideal model delta sinusoidal sigma weight residual 93.00 118.39 -25.39 1 1.00e+01 1.00e-02 9.27e+00 dihedral pdb=" CA SER A 47 " pdb=" C SER A 47 " pdb=" N PRO A 48 " pdb=" CA PRO A 48 " ideal model delta harmonic sigma weight residual 180.00 165.01 14.99 0 5.00e+00 4.00e-02 8.99e+00 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 395 0.037 - 0.074: 104 0.074 - 0.112: 22 0.112 - 0.149: 2 0.149 - 0.186: 2 Chirality restraints: 525 Sorted by residual: chirality pdb=" CA GLU A 257 " pdb=" N GLU A 257 " pdb=" C GLU A 257 " pdb=" CB GLU A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA GLU C 257 " pdb=" N GLU C 257 " pdb=" C GLU C 257 " pdb=" CB GLU C 257 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 chirality pdb=" CA GLU B 257 " pdb=" N GLU B 257 " pdb=" C GLU B 257 " pdb=" CB GLU B 257 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.52e-01 ... (remaining 522 not shown) Planarity restraints: 585 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU B 253 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.59e+00 pdb=" C GLU B 253 " -0.028 2.00e-02 2.50e+03 pdb=" O GLU B 253 " 0.010 2.00e-02 2.50e+03 pdb=" N THR B 254 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 268 " 0.022 5.00e-02 4.00e+02 3.30e-02 1.74e+00 pdb=" N PRO C 269 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA HIS C 45 " 0.006 2.00e-02 2.50e+03 1.31e-02 1.71e+00 pdb=" C HIS C 45 " -0.023 2.00e-02 2.50e+03 pdb=" O HIS C 45 " 0.008 2.00e-02 2.50e+03 pdb=" N CYS C 46 " 0.008 2.00e-02 2.50e+03 ... (remaining 582 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 825 2.79 - 3.32: 3428 3.32 - 3.85: 5678 3.85 - 4.37: 6494 4.37 - 4.90: 11051 Nonbonded interactions: 27476 Sorted by model distance: nonbonded pdb=" OG SER C 47 " pdb=" ND1 HIS C 50 " model vdw 2.264 3.120 nonbonded pdb=" OG SER B 47 " pdb=" ND1 HIS B 50 " model vdw 2.300 3.120 nonbonded pdb=" O PHE A 22 " pdb=" NH2 ARG A 238 " model vdw 2.301 3.120 nonbonded pdb=" O GLU A 62 " pdb=" OG1 THR A 65 " model vdw 2.302 3.040 nonbonded pdb=" OE2 GLU A 62 " pdb=" NZ LYS B 236 " model vdw 2.319 3.120 ... (remaining 27471 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 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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 individual isotropic 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: 3.490 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.510 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 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 : 0.002 0.022 3411 Z= 0.142 Angle : 0.522 6.373 4662 Z= 0.279 Chirality : 0.037 0.186 525 Planarity : 0.004 0.033 585 Dihedral : 12.414 61.325 1212 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.26 (0.43), residues: 402 helix: 1.50 (0.31), residues: 291 sheet: None (None), residues: 0 loop : 1.86 (0.65), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 265 HIS 0.003 0.001 HIS B 45 PHE 0.007 0.001 PHE A 237 TYR 0.006 0.001 TYR A 258 ARG 0.002 0.000 ARG A 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 5 LYS cc_start: 0.7412 (tmtt) cc_final: 0.6803 (tmtt) REVERT: C 233 MET cc_start: 0.8428 (mpp) cc_final: 0.7894 (mpp) outliers start: 0 outliers final: 0 residues processed: 42 average time/residue: 0.2428 time to fit residues: 11.9974 Evaluate side-chains 28 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 35 optimal weight: 10.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3411 Z= 0.271 Angle : 0.572 5.077 4662 Z= 0.302 Chirality : 0.040 0.147 525 Planarity : 0.005 0.040 585 Dihedral : 3.958 14.855 447 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.09 % Allowed : 6.83 % Favored : 92.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.50 (0.42), residues: 402 helix: 1.69 (0.30), residues: 291 sheet: None (None), residues: 0 loop : 1.91 (0.62), residues: 111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 60 HIS 0.005 0.001 HIS A 244 PHE 0.007 0.001 PHE B 237 TYR 0.009 0.001 TYR C 272 ARG 0.003 0.000 ARG B 238 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 31 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 233 MET cc_start: 0.8414 (mpp) cc_final: 0.7900 (mpp) outliers start: 4 outliers final: 4 residues processed: 33 average time/residue: 0.1907 time to fit residues: 7.6436 Evaluate side-chains 33 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 20 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 9 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.0020 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 overall best weight: 2.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3411 Z= 0.203 Angle : 0.540 5.397 4662 Z= 0.285 Chirality : 0.038 0.126 525 Planarity : 0.005 0.036 585 Dihedral : 3.934 14.848 447 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.64 % Allowed : 9.56 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.72 (0.43), residues: 402 helix: 1.85 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 2.01 (0.65), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.005 0.001 PHE C 16 TYR 0.007 0.001 TYR A 36 ARG 0.002 0.000 ARG A 238 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: C 233 MET cc_start: 0.8381 (mpp) cc_final: 0.7917 (mpp) outliers start: 6 outliers final: 4 residues processed: 29 average time/residue: 0.1708 time to fit residues: 6.2954 Evaluate side-chains 30 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain B residue 257 GLU Chi-restraints excluded: chain C residue 20 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 18 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 16 optimal weight: 9.9990 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 7.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.0870 chunk 0 optimal weight: 10.0000 overall best weight: 2.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN C 45 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3411 Z= 0.187 Angle : 0.530 5.496 4662 Z= 0.280 Chirality : 0.037 0.118 525 Planarity : 0.004 0.033 585 Dihedral : 3.908 14.960 447 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.19 % Allowed : 9.84 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.88 (0.43), residues: 402 helix: 1.96 (0.30), residues: 292 sheet: None (None), residues: 0 loop : 2.09 (0.65), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.005 0.001 PHE C 16 TYR 0.007 0.001 TYR C 272 ARG 0.002 0.000 ARG C 37 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 29 time to evaluate : 0.341 Fit side-chains REVERT: C 233 MET cc_start: 0.8309 (mpp) cc_final: 0.7961 (mpp) outliers start: 8 outliers final: 2 residues processed: 34 average time/residue: 0.1611 time to fit residues: 6.8528 Evaluate side-chains 29 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 32 optimal weight: 0.0980 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 0.0050 chunk 22 optimal weight: 0.9980 overall best weight: 1.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3411 Z= 0.166 Angle : 0.532 6.415 4662 Z= 0.280 Chirality : 0.037 0.136 525 Planarity : 0.004 0.033 585 Dihedral : 3.836 14.096 447 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.82 % Allowed : 11.75 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.92 (0.43), residues: 402 helix: 2.04 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.94 (0.66), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 60 HIS 0.003 0.001 HIS A 244 PHE 0.014 0.001 PHE B 237 TYR 0.008 0.001 TYR B 228 ARG 0.001 0.000 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.386 Fit side-chains REVERT: C 233 MET cc_start: 0.8257 (mpp) cc_final: 0.7954 (mpp) outliers start: 3 outliers final: 3 residues processed: 31 average time/residue: 0.1984 time to fit residues: 7.5481 Evaluate side-chains 30 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 20 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 9 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 36 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3411 Z= 0.266 Angle : 0.574 7.533 4662 Z= 0.296 Chirality : 0.039 0.130 525 Planarity : 0.005 0.040 585 Dihedral : 3.903 15.249 447 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.55 % Allowed : 13.93 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.88 (0.43), residues: 402 helix: 1.96 (0.31), residues: 292 sheet: None (None), residues: 0 loop : 2.09 (0.65), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.013 0.001 PHE B 237 TYR 0.010 0.001 TYR C 272 ARG 0.006 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.403 Fit side-chains REVERT: C 233 MET cc_start: 0.8287 (mpp) cc_final: 0.7955 (mpp) outliers start: 2 outliers final: 2 residues processed: 27 average time/residue: 0.1786 time to fit residues: 6.1632 Evaluate side-chains 28 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 21 optimal weight: 6.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 7.9990 chunk 23 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3411 Z= 0.196 Angle : 0.543 6.387 4662 Z= 0.283 Chirality : 0.037 0.129 525 Planarity : 0.004 0.034 585 Dihedral : 3.852 15.283 447 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.37 % Allowed : 13.66 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.93 (0.43), residues: 402 helix: 2.07 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.88 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.003 0.001 HIS A 244 PHE 0.012 0.001 PHE B 237 TYR 0.009 0.001 TYR B 228 ARG 0.004 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.445 Fit side-chains REVERT: C 44 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7297 (pp20) REVERT: C 233 MET cc_start: 0.8265 (mpp) cc_final: 0.7989 (mpp) outliers start: 5 outliers final: 2 residues processed: 31 average time/residue: 0.1770 time to fit residues: 7.1821 Evaluate side-chains 30 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 27 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 44 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 36 optimal weight: 0.2980 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 21 optimal weight: 9.9990 chunk 15 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3411 Z= 0.241 Angle : 0.578 6.934 4662 Z= 0.301 Chirality : 0.038 0.129 525 Planarity : 0.005 0.033 585 Dihedral : 3.855 15.666 447 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.09 % Allowed : 13.93 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.97 (0.43), residues: 402 helix: 2.11 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.87 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.012 0.001 PHE B 237 TYR 0.009 0.001 TYR C 272 ARG 0.003 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.382 Fit side-chains REVERT: B 257 GLU cc_start: 0.7470 (pp20) cc_final: 0.7267 (pp20) REVERT: C 233 MET cc_start: 0.8276 (mpp) cc_final: 0.7988 (mpp) outliers start: 4 outliers final: 3 residues processed: 30 average time/residue: 0.1711 time to fit residues: 6.5365 Evaluate side-chains 32 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 29 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 33 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 23 optimal weight: 5.9990 chunk 37 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 35 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3411 Z= 0.218 Angle : 0.580 7.230 4662 Z= 0.302 Chirality : 0.037 0.130 525 Planarity : 0.005 0.036 585 Dihedral : 3.846 15.679 447 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.09 % Allowed : 14.21 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.43), residues: 402 helix: 2.13 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.89 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.004 0.001 HIS A 244 PHE 0.011 0.001 PHE B 237 TYR 0.008 0.001 TYR C 272 ARG 0.003 0.000 ARG C 252 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.400 Fit side-chains REVERT: C 233 MET cc_start: 0.8265 (mpp) cc_final: 0.7989 (mpp) outliers start: 4 outliers final: 4 residues processed: 31 average time/residue: 0.1605 time to fit residues: 6.4030 Evaluate side-chains 33 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 23 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 31 optimal weight: 5.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3411 Z= 0.197 Angle : 0.604 7.458 4662 Z= 0.316 Chirality : 0.036 0.123 525 Planarity : 0.004 0.037 585 Dihedral : 3.806 14.745 447 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.09 % Allowed : 14.75 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.07 (0.43), residues: 402 helix: 2.16 (0.31), residues: 290 sheet: None (None), residues: 0 loop : 1.98 (0.65), residues: 112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 60 HIS 0.003 0.001 HIS A 244 PHE 0.011 0.001 PHE B 237 TYR 0.008 0.001 TYR A 228 ARG 0.003 0.000 ARG C 252 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 804 Ramachandran restraints generated. 402 Oldfield, 0 Emsley, 402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 32 time to evaluate : 0.369 Fit side-chains revert: symmetry clash REVERT: C 233 MET cc_start: 0.8197 (mpp) cc_final: 0.7986 (mpp) outliers start: 4 outliers final: 4 residues processed: 34 average time/residue: 0.1839 time to fit residues: 7.7444 Evaluate side-chains 33 residues out of total 366 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 29 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 257 GLU Chi-restraints excluded: chain A residue 267 ARG Chi-restraints excluded: chain B residue 45 HIS Chi-restraints excluded: chain C residue 14 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 3 optimal weight: 8.9990 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 7.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.053941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.043211 restraints weight = 16471.971| |-----------------------------------------------------------------------------| r_work (start): 0.3001 rms_B_bonded: 2.85 r_work: 0.2894 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 3411 Z= 0.345 Angle : 0.638 7.561 4662 Z= 0.335 Chirality : 0.041 0.135 525 Planarity : 0.005 0.037 585 Dihedral : 3.996 16.734 447 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.37 % Allowed : 14.21 % Favored : 84.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.84 (0.42), residues: 402 helix: 1.97 (0.31), residues: 292 sheet: None (None), residues: 0 loop : 1.94 (0.63), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 242 HIS 0.004 0.001 HIS A 244 PHE 0.012 0.002 PHE B 237 TYR 0.012 0.002 TYR C 272 ARG 0.002 0.000 ARG C 252 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1041.05 seconds wall clock time: 19 minutes 17.37 seconds (1157.37 seconds total)