Starting phenix.real_space_refine on Fri Aug 22 12:38:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x63_38078/08_2025/8x63_38078.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x63_38078/08_2025/8x63_38078.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8x63_38078/08_2025/8x63_38078.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x63_38078/08_2025/8x63_38078.map" model { file = "/net/cci-nas-00/data/ceres_data/8x63_38078/08_2025/8x63_38078.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x63_38078/08_2025/8x63_38078.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.056 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 20 5.16 5 C 1509 2.51 5 N 366 2.21 5 O 357 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2252 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2231 Classifications: {'peptide': 270} Link IDs: {'PTRANS': 10, 'TRANS': 259} Chain breaks: 2 Chain: "B" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'Y5E': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.03, per 1000 atoms: 0.46 Number of scatterers: 2252 At special positions: 0 Unit cell: (50.29, 75.97, 71.69, 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 20 16.00 O 357 8.00 N 366 7.00 C 1509 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.03 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " 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: 0.26 Conformation dependent library (CDL) restraints added in 84.6 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 524 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 0 sheets defined 86.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'B' and resid 27 through 55 removed outlier: 3.715A pdb=" N VAL B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N THR B 36 " --> pdb=" O VAL B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 90 Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 96 through 129 removed outlier: 3.537A pdb=" N CYS B 100 " --> pdb=" O GLY B 96 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N PHE B 119 " --> pdb=" O ILE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 164 Proline residue: B 161 - end of helix removed outlier: 3.908A pdb=" N GLY B 164 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 186 removed outlier: 3.534A pdb=" N TYR B 185 " --> pdb=" O THR B 182 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N ASP B 186 " --> pdb=" O ASP B 183 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 182 through 186' Processing helix chain 'B' and resid 187 through 221 removed outlier: 3.949A pdb=" N LYS B 191 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 427 Processing helix chain 'B' and resid 428 through 441 removed outlier: 3.521A pdb=" N ALA B 439 " --> pdb=" O PHE B 435 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N PHE B 440 " --> pdb=" O MET B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 445 removed outlier: 3.832A pdb=" N CYS B 445 " --> pdb=" O LYS B 442 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 442 through 445' Processing helix chain 'B' and resid 446 through 472 Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix removed outlier: 4.076A pdb=" N ASN B 472 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 4.135A pdb=" N LYS B 476 " --> pdb=" O ASN B 472 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 477 " --> pdb=" O GLU B 473 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ARG B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) 161 hydrogen bonds defined for protein. 483 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: 0.37 Time building geometry restraints manager: 0.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 314 1.29 - 1.42: 669 1.42 - 1.55: 1299 1.55 - 1.68: 2 1.68 - 1.81: 31 Bond restraints: 2315 Sorted by residual: bond pdb=" C PHE B 424 " pdb=" N ILE B 425 " ideal model delta sigma weight residual 1.331 1.246 0.085 1.42e-02 4.96e+03 3.60e+01 bond pdb=" C ILE B 115 " pdb=" O ILE B 115 " ideal model delta sigma weight residual 1.236 1.170 0.066 1.19e-02 7.06e+03 3.09e+01 bond pdb=" C14 Y5E B 601 " pdb=" N08 Y5E B 601 " ideal model delta sigma weight residual 1.368 1.477 -0.109 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C PHE B 424 " pdb=" O PHE B 424 " ideal model delta sigma weight residual 1.236 1.160 0.076 1.47e-02 4.63e+03 2.65e+01 bond pdb=" N PHE B 424 " pdb=" CA PHE B 424 " ideal model delta sigma weight residual 1.457 1.509 -0.052 1.40e-02 5.10e+03 1.40e+01 ... (remaining 2310 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 2980 1.42 - 2.84: 113 2.84 - 4.26: 26 4.26 - 5.68: 14 5.68 - 7.10: 7 Bond angle restraints: 3140 Sorted by residual: angle pdb=" C PHE B 424 " pdb=" N ILE B 425 " pdb=" CA ILE B 425 " ideal model delta sigma weight residual 122.97 116.24 6.73 9.80e-01 1.04e+00 4.71e+01 angle pdb=" N VAL B 129 " pdb=" CA VAL B 129 " pdb=" C VAL B 129 " ideal model delta sigma weight residual 111.77 105.86 5.91 1.04e+00 9.25e-01 3.23e+01 angle pdb=" O ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 122.07 116.28 5.79 1.03e+00 9.43e-01 3.16e+01 angle pdb=" CA ALA B 423 " pdb=" C ALA B 423 " pdb=" N PHE B 424 " ideal model delta sigma weight residual 117.07 122.70 -5.63 1.14e+00 7.69e-01 2.44e+01 angle pdb=" O SER B 114 " pdb=" C SER B 114 " pdb=" N ILE B 115 " ideal model delta sigma weight residual 122.03 116.85 5.18 1.08e+00 8.57e-01 2.30e+01 ... (remaining 3135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.56: 1183 16.56 - 33.12: 136 33.12 - 49.68: 32 49.68 - 66.24: 6 66.24 - 82.80: 3 Dihedral angle restraints: 1360 sinusoidal: 555 harmonic: 805 Sorted by residual: dihedral pdb=" N PHE B 424 " pdb=" C PHE B 424 " pdb=" CA PHE B 424 " pdb=" CB PHE B 424 " ideal model delta harmonic sigma weight residual 122.80 135.14 -12.34 0 2.50e+00 1.60e-01 2.44e+01 dihedral pdb=" C PHE B 424 " pdb=" N PHE B 424 " pdb=" CA PHE B 424 " pdb=" CB PHE B 424 " ideal model delta harmonic sigma weight residual -122.60 -134.83 12.23 0 2.50e+00 1.60e-01 2.39e+01 dihedral pdb=" CA ILE B 115 " pdb=" C ILE B 115 " pdb=" N PHE B 116 " pdb=" CA PHE B 116 " ideal model delta harmonic sigma weight residual 180.00 158.22 21.78 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 1357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 346 0.098 - 0.196: 9 0.196 - 0.293: 0 0.293 - 0.391: 0 0.391 - 0.488: 2 Chirality restraints: 357 Sorted by residual: chirality pdb=" CA PHE B 424 " pdb=" N PHE B 424 " pdb=" C PHE B 424 " pdb=" CB PHE B 424 " both_signs ideal model delta sigma weight residual False 2.51 2.02 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.02 0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA VAL B 129 " pdb=" N VAL B 129 " pdb=" C VAL B 129 " pdb=" CB VAL B 129 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.82e-01 ... (remaining 354 not shown) Planarity restraints: 371 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 424 " 0.023 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C PHE B 424 " -0.079 2.00e-02 2.50e+03 pdb=" O PHE B 424 " 0.030 2.00e-02 2.50e+03 pdb=" N ILE B 425 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 114 " -0.019 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C SER B 114 " 0.062 2.00e-02 2.50e+03 pdb=" O SER B 114 " -0.022 2.00e-02 2.50e+03 pdb=" N ILE B 115 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 115 " 0.018 2.00e-02 2.50e+03 3.54e-02 1.25e+01 pdb=" C ILE B 115 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE B 115 " 0.022 2.00e-02 2.50e+03 pdb=" N PHE B 116 " 0.021 2.00e-02 2.50e+03 ... (remaining 368 not shown) Histogram of nonbonded interaction distances: 2.41 - 2.91: 881 2.91 - 3.41: 2385 3.41 - 3.90: 3516 3.90 - 4.40: 3884 4.40 - 4.90: 6390 Nonbonded interactions: 17056 Sorted by model distance: nonbonded pdb=" O PHE B 424 " pdb=" CG PHE B 424 " model vdw 2.411 3.260 nonbonded pdb=" O ASN B 408 " pdb=" N ARG B 411 " model vdw 2.513 3.120 nonbonded pdb=" O HIS B 450 " pdb=" OG1 THR B 453 " model vdw 2.516 3.040 nonbonded pdb=" O PHE B 424 " pdb=" CD1 PHE B 424 " model vdw 2.519 3.340 nonbonded pdb=" CG2 ILE B 115 " pdb=" CD1 ILE B 115 " model vdw 2.520 3.104 ... (remaining 17051 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.00 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: 1.440 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: 0.040 Check model and map are aligned: 0.000 Set scattering table: 0.020 Process input model: 5.040 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.1172 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 0.109 2317 Z= 0.341 Angle : 0.773 7.099 3144 Z= 0.459 Chirality : 0.055 0.488 357 Planarity : 0.007 0.051 371 Dihedral : 15.286 82.798 830 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 0.81 % Allowed : 0.41 % Favored : 98.78 % Cbeta Deviations : 0.38 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.52), residues: 264 helix: 1.06 (0.37), residues: 196 sheet: None (None), residues: 0 loop : -3.58 (0.62), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 481 TYR 0.011 0.001 TYR B 214 PHE 0.027 0.002 PHE B 435 TRP 0.008 0.001 TRP B 165 HIS 0.009 0.002 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 2315) covalent geometry : angle 0.77324 ( 3140) SS BOND : bond 0.00253 ( 2) SS BOND : angle 0.52317 ( 4) hydrogen bonds : bond 0.13054 ( 161) hydrogen bonds : angle 5.80917 ( 483) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.141 Fit side-chains REVERT: B 45 ASN cc_start: 0.2777 (m-40) cc_final: 0.2053 (m110) outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.0764 time to fit residues: 2.5561 Evaluate side-chains 18 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 17 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 13 optimal weight: 0.0000 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.2980 chunk 15 optimal weight: 0.7980 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.224396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.193562 restraints weight = 2527.681| |-----------------------------------------------------------------------------| r_work (start): 0.4228 rms_B_bonded: 3.42 r_work: 0.4055 rms_B_bonded: 4.47 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2176 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 2317 Z= 0.228 Angle : 0.835 8.337 3144 Z= 0.423 Chirality : 0.047 0.165 357 Planarity : 0.007 0.060 371 Dihedral : 5.356 22.144 308 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 0.41 % Allowed : 10.98 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.50), residues: 264 helix: 0.66 (0.35), residues: 210 sheet: None (None), residues: 0 loop : -4.26 (0.62), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 97 TYR 0.010 0.002 TYR B 50 PHE 0.019 0.002 PHE B 432 TRP 0.042 0.004 TRP B 93 HIS 0.002 0.001 HIS B 450 Details of bonding type rmsd covalent geometry : bond 0.00482 ( 2315) covalent geometry : angle 0.83527 ( 3140) SS BOND : bond 0.00776 ( 2) SS BOND : angle 0.69742 ( 4) hydrogen bonds : bond 0.05952 ( 161) hydrogen bonds : angle 5.08436 ( 483) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 18 time to evaluate : 0.085 Fit side-chains REVERT: B 436 MET cc_start: 0.5825 (ptp) cc_final: 0.5433 (ptp) outliers start: 1 outliers final: 1 residues processed: 18 average time/residue: 0.0465 time to fit residues: 1.1500 Evaluate side-chains 16 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 15 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 4 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 21 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4604 r_free = 0.4604 target = 0.239312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.213685 restraints weight = 2759.105| |-----------------------------------------------------------------------------| r_work (start): 0.4402 rms_B_bonded: 3.41 r_work: 0.4253 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.4253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3316 moved from start: 0.7948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 2317 Z= 0.250 Angle : 0.926 13.741 3144 Z= 0.465 Chirality : 0.050 0.178 357 Planarity : 0.006 0.052 371 Dihedral : 7.452 49.481 306 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.25 % Allowed : 15.45 % Favored : 81.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.51), residues: 264 helix: 0.18 (0.35), residues: 210 sheet: None (None), residues: 0 loop : -4.61 (0.64), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 219 TYR 0.017 0.002 TYR B 214 PHE 0.011 0.002 PHE B 116 TRP 0.045 0.004 TRP B 93 HIS 0.007 0.002 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00533 ( 2315) covalent geometry : angle 0.92480 ( 3140) SS BOND : bond 0.00045 ( 2) SS BOND : angle 1.38725 ( 4) hydrogen bonds : bond 0.06188 ( 161) hydrogen bonds : angle 5.35330 ( 483) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 29 time to evaluate : 0.086 Fit side-chains REVERT: B 93 TRP cc_start: 0.4502 (t-100) cc_final: 0.4061 (t-100) REVERT: B 169 MET cc_start: 0.2071 (mmm) cc_final: 0.1477 (mtm) outliers start: 8 outliers final: 3 residues processed: 35 average time/residue: 0.0598 time to fit residues: 2.5628 Evaluate side-chains 23 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 20 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 182 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.2980 chunk 3 optimal weight: 0.0970 chunk 9 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 0.6980 chunk 1 optimal weight: 0.0980 chunk 0 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 overall best weight: 0.3578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.264009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.237253 restraints weight = 2668.293| |-----------------------------------------------------------------------------| r_work (start): 0.4678 rms_B_bonded: 3.18 r_work: 0.4543 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.4543 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3336 moved from start: 0.9712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2317 Z= 0.193 Angle : 0.724 6.734 3144 Z= 0.374 Chirality : 0.044 0.124 357 Planarity : 0.006 0.064 371 Dihedral : 5.451 22.041 306 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.25 % Allowed : 22.36 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.63 (0.52), residues: 264 helix: 0.60 (0.35), residues: 212 sheet: None (None), residues: 0 loop : -4.73 (0.62), residues: 52 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 53 TYR 0.015 0.002 TYR B 468 PHE 0.005 0.001 PHE B 432 TRP 0.033 0.003 TRP B 93 HIS 0.006 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 2315) covalent geometry : angle 0.72408 ( 3140) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.32135 ( 4) hydrogen bonds : bond 0.05039 ( 161) hydrogen bonds : angle 4.79235 ( 483) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 25 time to evaluate : 0.088 Fit side-chains REVERT: B 56 ARG cc_start: 0.3747 (mmt90) cc_final: 0.2539 (tpt170) REVERT: B 97 ARG cc_start: 0.4610 (ttp80) cc_final: 0.3931 (ptm160) REVERT: B 169 MET cc_start: 0.2431 (mmm) cc_final: 0.1506 (mtm) REVERT: B 208 TRP cc_start: 0.4636 (OUTLIER) cc_final: 0.3778 (t-100) REVERT: B 221 LEU cc_start: 0.2447 (OUTLIER) cc_final: 0.2027 (pp) outliers start: 8 outliers final: 4 residues processed: 31 average time/residue: 0.0630 time to fit residues: 2.3826 Evaluate side-chains 30 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 221 LEU Chi-restraints excluded: chain B residue 416 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 24 optimal weight: 0.5980 chunk 19 optimal weight: 0.0670 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 6 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4787 r_free = 0.4787 target = 0.254347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.223640 restraints weight = 2701.019| |-----------------------------------------------------------------------------| r_work (start): 0.4506 rms_B_bonded: 3.30 r_work: 0.4372 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3971 moved from start: 1.3154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 2317 Z= 0.222 Angle : 0.826 9.639 3144 Z= 0.436 Chirality : 0.050 0.155 357 Planarity : 0.006 0.059 371 Dihedral : 6.976 30.498 306 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 6.10 % Allowed : 23.98 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.87 (0.51), residues: 264 helix: 0.40 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -4.58 (0.62), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 53 TYR 0.015 0.002 TYR B 138 PHE 0.019 0.002 PHE B 432 TRP 0.020 0.002 TRP B 428 HIS 0.008 0.002 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00493 ( 2315) covalent geometry : angle 0.82657 ( 3140) SS BOND : bond 0.00229 ( 2) SS BOND : angle 0.30028 ( 4) hydrogen bonds : bond 0.05964 ( 161) hydrogen bonds : angle 5.04162 ( 483) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 29 time to evaluate : 0.089 Fit side-chains REVERT: B 53 ARG cc_start: 0.6277 (mmm-85) cc_final: 0.5518 (tpt90) REVERT: B 95 LEU cc_start: 0.6709 (OUTLIER) cc_final: 0.6505 (tp) REVERT: B 97 ARG cc_start: 0.5589 (ttp80) cc_final: 0.5303 (ptm160) REVERT: B 99 LEU cc_start: 0.1662 (OUTLIER) cc_final: 0.1335 (tt) REVERT: B 169 MET cc_start: 0.3109 (mmm) cc_final: 0.2663 (mtt) REVERT: B 193 MET cc_start: 0.3602 (ttm) cc_final: 0.3247 (mtt) outliers start: 15 outliers final: 8 residues processed: 39 average time/residue: 0.0599 time to fit residues: 2.8527 Evaluate side-chains 36 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 26 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 95 LEU Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 208 TRP Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 420 ILE Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 3 optimal weight: 0.0870 chunk 11 optimal weight: 0.4980 chunk 14 optimal weight: 0.7980 chunk 4 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 166 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.248131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.215093 restraints weight = 2657.774| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.45 r_work: 0.4255 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4080 moved from start: 1.4167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 2317 Z= 0.192 Angle : 0.732 6.963 3144 Z= 0.381 Chirality : 0.045 0.144 357 Planarity : 0.005 0.053 371 Dihedral : 5.699 24.736 306 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.44 % Allowed : 27.64 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.79 (0.50), residues: 264 helix: 0.41 (0.35), residues: 211 sheet: None (None), residues: 0 loop : -4.25 (0.68), residues: 53 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 143 TYR 0.009 0.002 TYR B 200 PHE 0.007 0.001 PHE B 432 TRP 0.025 0.003 TRP B 93 HIS 0.006 0.002 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 2315) covalent geometry : angle 0.73020 ( 3140) SS BOND : bond 0.00456 ( 2) SS BOND : angle 1.49120 ( 4) hydrogen bonds : bond 0.05171 ( 161) hydrogen bonds : angle 4.77912 ( 483) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 24 time to evaluate : 0.083 Fit side-chains REVERT: B 53 ARG cc_start: 0.6156 (mmm-85) cc_final: 0.5790 (tpt90) REVERT: B 97 ARG cc_start: 0.6147 (ttp80) cc_final: 0.5902 (ttt180) REVERT: B 169 MET cc_start: 0.3315 (mmm) cc_final: 0.2952 (mtt) outliers start: 6 outliers final: 5 residues processed: 29 average time/residue: 0.0723 time to fit residues: 2.4848 Evaluate side-chains 28 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 23 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 25 optimal weight: 0.2980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4642 r_free = 0.4642 target = 0.237228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.201144 restraints weight = 2598.607| |-----------------------------------------------------------------------------| r_work (start): 0.4257 rms_B_bonded: 3.42 r_work: 0.4114 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.4114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4374 moved from start: 1.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 2317 Z= 0.228 Angle : 0.838 10.753 3144 Z= 0.453 Chirality : 0.049 0.169 357 Planarity : 0.006 0.058 371 Dihedral : 6.979 40.719 306 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 4.07 % Allowed : 26.42 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.50), residues: 264 helix: 0.30 (0.35), residues: 210 sheet: None (None), residues: 0 loop : -4.31 (0.65), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 143 TYR 0.016 0.002 TYR B 138 PHE 0.016 0.002 PHE B 199 TRP 0.023 0.003 TRP B 93 HIS 0.009 0.002 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00502 ( 2315) covalent geometry : angle 0.83890 ( 3140) SS BOND : bond 0.00168 ( 2) SS BOND : angle 0.28556 ( 4) hydrogen bonds : bond 0.05754 ( 161) hydrogen bonds : angle 5.21761 ( 483) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 25 time to evaluate : 0.081 Fit side-chains REVERT: B 53 ARG cc_start: 0.6300 (mmm-85) cc_final: 0.6033 (tpt90) REVERT: B 83 MET cc_start: 0.3426 (tmm) cc_final: 0.3049 (mtt) REVERT: B 99 LEU cc_start: 0.2334 (OUTLIER) cc_final: 0.2133 (tt) outliers start: 10 outliers final: 6 residues processed: 32 average time/residue: 0.0646 time to fit residues: 2.5091 Evaluate side-chains 29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 22 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 203 THR Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 19 optimal weight: 0.0980 chunk 21 optimal weight: 0.4980 chunk 11 optimal weight: 0.8980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.237982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.201659 restraints weight = 2568.771| |-----------------------------------------------------------------------------| r_work (start): 0.4260 rms_B_bonded: 3.39 r_work: 0.4123 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.4123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4375 moved from start: 1.7569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2317 Z= 0.171 Angle : 0.715 8.077 3144 Z= 0.364 Chirality : 0.044 0.143 357 Planarity : 0.005 0.053 371 Dihedral : 5.622 22.076 306 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.66 % Allowed : 26.42 % Favored : 69.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.50), residues: 264 helix: 0.52 (0.35), residues: 210 sheet: None (None), residues: 0 loop : -4.34 (0.63), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 411 TYR 0.013 0.002 TYR B 431 PHE 0.015 0.001 PHE B 432 TRP 0.025 0.003 TRP B 93 HIS 0.007 0.002 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 2315) covalent geometry : angle 0.71458 ( 3140) SS BOND : bond 0.00183 ( 2) SS BOND : angle 1.14120 ( 4) hydrogen bonds : bond 0.04902 ( 161) hydrogen bonds : angle 4.70777 ( 483) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 22 time to evaluate : 0.078 Fit side-chains REVERT: B 83 MET cc_start: 0.3888 (tmm) cc_final: 0.3629 (mtt) REVERT: B 106 MET cc_start: 0.5235 (OUTLIER) cc_final: 0.4831 (tpp) outliers start: 9 outliers final: 5 residues processed: 30 average time/residue: 0.0494 time to fit residues: 1.8737 Evaluate side-chains 26 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 20 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Chi-restraints excluded: chain B residue 432 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 15 optimal weight: 0.0070 chunk 19 optimal weight: 0.0670 chunk 18 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 overall best weight: 0.2694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4666 r_free = 0.4666 target = 0.240489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.204135 restraints weight = 2589.966| |-----------------------------------------------------------------------------| r_work (start): 0.4300 rms_B_bonded: 3.42 r_work: 0.4158 rms_B_bonded: 4.74 restraints_weight: 0.5000 r_work (final): 0.4158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4356 moved from start: 1.7894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2317 Z= 0.149 Angle : 0.681 7.291 3144 Z= 0.347 Chirality : 0.040 0.127 357 Planarity : 0.005 0.046 371 Dihedral : 5.259 22.621 306 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.44 % Allowed : 26.02 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.35 (0.52), residues: 264 helix: 0.81 (0.36), residues: 210 sheet: None (None), residues: 0 loop : -4.50 (0.61), residues: 54 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 53 TYR 0.016 0.002 TYR B 431 PHE 0.010 0.001 PHE B 435 TRP 0.019 0.003 TRP B 93 HIS 0.005 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 2315) covalent geometry : angle 0.68067 ( 3140) SS BOND : bond 0.00163 ( 2) SS BOND : angle 1.02557 ( 4) hydrogen bonds : bond 0.04690 ( 161) hydrogen bonds : angle 4.54531 ( 483) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 23 time to evaluate : 0.093 Fit side-chains REVERT: B 81 MET cc_start: 0.4494 (mtp) cc_final: 0.3014 (ttp) REVERT: B 93 TRP cc_start: 0.7014 (t60) cc_final: 0.6618 (t60) REVERT: B 106 MET cc_start: 0.5017 (OUTLIER) cc_final: 0.4628 (tpp) REVERT: B 435 PHE cc_start: 0.5215 (m-80) cc_final: 0.4833 (m-80) outliers start: 6 outliers final: 4 residues processed: 28 average time/residue: 0.0355 time to fit residues: 1.3565 Evaluate side-chains 27 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 0.0870 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.221942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4146 r_free = 0.4146 target = 0.183636 restraints weight = 2583.469| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 3.41 r_work: 0.3957 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4370 moved from start: 1.9108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 2317 Z= 0.184 Angle : 0.729 8.020 3144 Z= 0.377 Chirality : 0.045 0.198 357 Planarity : 0.005 0.048 371 Dihedral : 5.742 27.779 306 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.85 % Allowed : 26.42 % Favored : 70.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.51), residues: 264 helix: 0.58 (0.35), residues: 207 sheet: None (None), residues: 0 loop : -4.56 (0.61), residues: 57 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 139 TYR 0.016 0.002 TYR B 431 PHE 0.019 0.002 PHE B 435 TRP 0.039 0.003 TRP B 93 HIS 0.007 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 2315) covalent geometry : angle 0.72911 ( 3140) SS BOND : bond 0.00139 ( 2) SS BOND : angle 0.63885 ( 4) hydrogen bonds : bond 0.05067 ( 161) hydrogen bonds : angle 4.78745 ( 483) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 528 Ramachandran restraints generated. 264 Oldfield, 0 Emsley, 264 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.048 Fit side-chains REVERT: B 55 GLU cc_start: 0.5987 (tp30) cc_final: 0.4973 (tt0) outliers start: 7 outliers final: 6 residues processed: 33 average time/residue: 0.0431 time to fit residues: 1.7720 Evaluate side-chains 32 residues out of total 246 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 26 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 MET Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 193 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 416 GLN Chi-restraints excluded: chain B residue 429 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.1980 chunk 26 optimal weight: 0.0370 chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 18 optimal weight: 0.4980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 0.0040 chunk 17 optimal weight: 0.3980 chunk 2 optimal weight: 0.8980 chunk 10 optimal weight: 0.4980 overall best weight: 0.2070 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4615 r_free = 0.4615 target = 0.235459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.199819 restraints weight = 2597.011| |-----------------------------------------------------------------------------| r_work (start): 0.4219 rms_B_bonded: 3.48 r_work: 0.4075 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.4075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4458 moved from start: 1.9281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2317 Z= 0.142 Angle : 0.670 6.766 3144 Z= 0.341 Chirality : 0.040 0.124 357 Planarity : 0.005 0.036 371 Dihedral : 5.017 21.140 306 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.03 % Allowed : 26.42 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.23 (0.52), residues: 264 helix: 0.94 (0.36), residues: 208 sheet: None (None), residues: 0 loop : -4.49 (0.61), residues: 56 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 411 TYR 0.025 0.002 TYR B 431 PHE 0.014 0.001 PHE B 435 TRP 0.026 0.003 TRP B 93 HIS 0.005 0.001 HIS B 59 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 2315) covalent geometry : angle 0.67033 ( 3140) SS BOND : bond 0.00171 ( 2) SS BOND : angle 0.56721 ( 4) hydrogen bonds : bond 0.04637 ( 161) hydrogen bonds : angle 4.47360 ( 483) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 884.97 seconds wall clock time: 16 minutes 17.66 seconds (977.66 seconds total)