Starting phenix.real_space_refine on Wed Sep 17 03:16:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iqr_60793/09_2025/9iqr_60793.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iqr_60793/09_2025/9iqr_60793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iqr_60793/09_2025/9iqr_60793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iqr_60793/09_2025/9iqr_60793.map" model { file = "/net/cci-nas-00/data/ceres_data/9iqr_60793/09_2025/9iqr_60793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iqr_60793/09_2025/9iqr_60793.cif" } resolution = 3.4 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= -0.001 sd= 0.062 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 21 5.16 5 C 1735 2.51 5 N 430 2.21 5 O 436 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2622 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 512 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain: "B" Number of atoms: 2110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 2110 Classifications: {'peptide': 260} Link IDs: {'PTRANS': 10, 'TRANS': 249} Chain breaks: 2 Time building chain proxies: 0.94, per 1000 atoms: 0.36 Number of scatterers: 2622 At special positions: 0 Unit cell: (51.36, 72.76, 94.16, 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 21 16.00 O 436 8.00 N 430 7.00 C 1735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 3 " - pdb=" SG CYS A 24 " distance=2.03 Simple disulfide: pdb=" SG CYS A 17 " - pdb=" SG CYS A 42 " distance=2.03 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 57 " distance=2.03 Simple disulfide: pdb=" SG CYS A 58 " - pdb=" SG CYS A 63 " distance=2.03 Simple disulfide: pdb=" SG CYS B 121 " - pdb=" SG CYS B 203 " 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: 0.21 Conformation dependent library (CDL) restraints added in 84.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 626 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 2 sheets defined 69.5% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.05 Creating SS restraints... Processing helix chain 'B' and resid 47 through 74 Processing helix chain 'B' and resid 84 through 98 removed outlier: 3.939A pdb=" N VAL B 88 " --> pdb=" O ASN B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 112 Processing helix chain 'B' and resid 117 through 153 removed outlier: 3.709A pdb=" N CYS B 132 " --> pdb=" O ASP B 128 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 153 " --> pdb=" O SER B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 160 through 179 removed outlier: 3.543A pdb=" N ARG B 164 " --> pdb=" O ARG B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 187 removed outlier: 3.556A pdb=" N LEU B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 220 Processing helix chain 'B' and resid 220 through 241 Processing helix chain 'B' and resid 382 through 415 Proline residue: B 404 - end of helix Processing helix chain 'B' and resid 419 through 444 removed outlier: 3.818A pdb=" N GLY B 430 " --> pdb=" O PHE B 426 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N TYR B 431 " --> pdb=" O PHE B 427 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER B 435 " --> pdb=" O TYR B 431 " (cutoff:3.500A) Proline residue: B 438 - end of helix Processing helix chain 'B' and resid 445 through 454 Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 5.052A pdb=" N VAL A 4 " --> pdb=" O GLU A 15 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N GLU A 15 " --> pdb=" O VAL A 4 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 43 removed outlier: 6.714A pdb=" N TYR A 35 " --> pdb=" O VAL A 31 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 537 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: 0.30 Time building geometry restraints manager: 0.29 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: 784 1.35 - 1.47: 724 1.47 - 1.59: 1160 1.59 - 1.71: 0 1.71 - 1.83: 24 Bond restraints: 2692 Sorted by residual: bond pdb=" CA ASN B 437 " pdb=" C ASN B 437 " ideal model delta sigma weight residual 1.520 1.533 -0.013 1.23e-02 6.61e+03 1.13e+00 bond pdb=" CG LEU B 90 " pdb=" CD1 LEU B 90 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.64e-01 bond pdb=" CB ASN B 108 " pdb=" CG ASN B 108 " ideal model delta sigma weight residual 1.516 1.537 -0.021 2.50e-02 1.60e+03 7.34e-01 bond pdb=" CG1 ILE B 395 " pdb=" CD1 ILE B 395 " ideal model delta sigma weight residual 1.513 1.484 0.029 3.90e-02 6.57e+02 5.41e-01 bond pdb=" C PRO B 182 " pdb=" N PRO B 183 " ideal model delta sigma weight residual 1.335 1.344 -0.009 1.28e-02 6.10e+03 5.23e-01 ... (remaining 2687 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.19: 3495 1.19 - 2.39: 138 2.39 - 3.58: 18 3.58 - 4.77: 6 4.77 - 5.96: 7 Bond angle restraints: 3664 Sorted by residual: angle pdb=" N PRO B 182 " pdb=" CA PRO B 182 " pdb=" C PRO B 182 " ideal model delta sigma weight residual 110.70 113.07 -2.37 1.22e+00 6.72e-01 3.79e+00 angle pdb=" CA PRO B 182 " pdb=" C PRO B 182 " pdb=" N PRO B 183 " ideal model delta sigma weight residual 117.93 120.00 -2.07 1.20e+00 6.94e-01 2.96e+00 angle pdb=" CB GLU B 109 " pdb=" CG GLU B 109 " pdb=" CD GLU B 109 " ideal model delta sigma weight residual 112.60 115.51 -2.91 1.70e+00 3.46e-01 2.92e+00 angle pdb=" C GLU B 155 " pdb=" N TYR B 156 " pdb=" CA TYR B 156 " ideal model delta sigma weight residual 121.54 124.68 -3.14 1.91e+00 2.74e-01 2.70e+00 angle pdb=" N ILE A 55 " pdb=" CA ILE A 55 " pdb=" C ILE A 55 " ideal model delta sigma weight residual 107.18 109.99 -2.81 1.73e+00 3.34e-01 2.63e+00 ... (remaining 3659 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1421 17.98 - 35.96: 135 35.96 - 53.94: 27 53.94 - 71.93: 1 71.93 - 89.91: 1 Dihedral angle restraints: 1585 sinusoidal: 624 harmonic: 961 Sorted by residual: dihedral pdb=" CB CYS A 58 " pdb=" SG CYS A 58 " pdb=" SG CYS A 63 " pdb=" CB CYS A 63 " ideal model delta sinusoidal sigma weight residual -86.00 -38.44 -47.56 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CA THR B 99 " pdb=" C THR B 99 " pdb=" N LEU B 100 " pdb=" CA LEU B 100 " ideal model delta harmonic sigma weight residual 180.00 161.25 18.75 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CA CYS B 203 " pdb=" C CYS B 203 " pdb=" N GLU B 204 " pdb=" CA GLU B 204 " ideal model delta harmonic sigma weight residual -180.00 -164.59 -15.41 0 5.00e+00 4.00e-02 9.50e+00 ... (remaining 1582 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 364 0.061 - 0.121: 61 0.121 - 0.182: 3 0.182 - 0.242: 0 0.242 - 0.303: 1 Chirality restraints: 429 Sorted by residual: chirality pdb=" CB ILE B 169 " pdb=" CA ILE B 169 " pdb=" CG1 ILE B 169 " pdb=" CG2 ILE B 169 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CB ILE A 55 " pdb=" CA ILE A 55 " pdb=" CG1 ILE A 55 " pdb=" CG2 ILE A 55 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA THR B 161 " pdb=" N THR B 161 " pdb=" C THR B 161 " pdb=" CB THR B 161 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.14 2.00e-01 2.50e+01 4.80e-01 ... (remaining 426 not shown) Planarity restraints: 443 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE A 32 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 33 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 33 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 33 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 46 " -0.025 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO A 47 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 47 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 47 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 418 " 0.022 5.00e-02 4.00e+02 3.33e-02 1.77e+00 pdb=" N PRO B 419 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO B 419 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 419 " 0.018 5.00e-02 4.00e+02 ... (remaining 440 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 745 2.82 - 3.34: 2669 3.34 - 3.86: 4378 3.86 - 4.38: 4687 4.38 - 4.90: 8148 Nonbonded interactions: 20627 Sorted by model distance: nonbonded pdb=" NH2 ARG B 383 " pdb=" OD2 ASP B 447 " model vdw 2.294 3.120 nonbonded pdb=" O THR B 62 " pdb=" ND2 ASN B 66 " model vdw 2.308 3.120 nonbonded pdb=" OG1 THR A 8 " pdb=" O ALA B 413 " model vdw 2.311 3.040 nonbonded pdb=" NH2 ARG A 27 " pdb=" OE2 GLU A 50 " model vdw 2.313 3.120 nonbonded pdb=" O THR A 36 " pdb=" OG1 THR A 36 " model vdw 2.356 3.040 ... (remaining 20622 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.240 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: 0.010 Process input model: 4.180 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 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 : 0.003 0.032 2697 Z= 0.143 Angle : 0.584 5.965 3674 Z= 0.309 Chirality : 0.045 0.303 429 Planarity : 0.005 0.049 443 Dihedral : 13.666 89.907 944 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % 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 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: 1.59 (0.49), residues: 317 helix: 2.64 (0.35), residues: 215 sheet: -0.48 (1.05), residues: 25 loop : -3.36 (0.59), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 420 TYR 0.017 0.001 TYR B 409 PHE 0.020 0.001 PHE B 429 TRP 0.019 0.001 TRP B 173 HIS 0.002 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 2692) covalent geometry : angle 0.57726 ( 3664) SS BOND : bond 0.00175 ( 5) SS BOND : angle 1.79714 ( 10) hydrogen bonds : bond 0.11159 ( 180) hydrogen bonds : angle 4.77939 ( 537) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.088 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 63 average time/residue: 0.0429 time to fit residues: 3.4022 Evaluate side-chains 52 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 22 optimal weight: 0.0770 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.166716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.133824 restraints weight = 3883.827| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.55 r_work: 0.3585 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2697 Z= 0.137 Angle : 0.554 6.204 3674 Z= 0.296 Chirality : 0.044 0.168 429 Planarity : 0.005 0.047 443 Dihedral : 4.012 16.763 353 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.06 % Allowed : 11.68 % Favored : 86.25 % 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: 1.73 (0.48), residues: 317 helix: 2.70 (0.34), residues: 215 sheet: -0.31 (1.04), residues: 25 loop : -3.19 (0.57), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 383 TYR 0.014 0.002 TYR B 441 PHE 0.014 0.001 PHE B 429 TRP 0.013 0.001 TRP B 173 HIS 0.006 0.002 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 2692) covalent geometry : angle 0.55189 ( 3664) SS BOND : bond 0.00242 ( 5) SS BOND : angle 1.00717 ( 10) hydrogen bonds : bond 0.04378 ( 180) hydrogen bonds : angle 4.01577 ( 537) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.057 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.0287 time to fit residues: 1.9955 Evaluate side-chains 49 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 46 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 159 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 8.9990 chunk 16 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 8.9990 chunk 31 optimal weight: 0.7980 chunk 2 optimal weight: 6.9990 chunk 14 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN B 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.165475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.132405 restraints weight = 3975.420| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 2.61 r_work: 0.3575 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2697 Z= 0.135 Angle : 0.534 6.232 3674 Z= 0.282 Chirality : 0.043 0.138 429 Planarity : 0.005 0.047 443 Dihedral : 3.887 17.013 353 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 3.44 % Allowed : 15.81 % Favored : 80.76 % 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: 1.82 (0.49), residues: 317 helix: 2.75 (0.34), residues: 215 sheet: -0.09 (1.05), residues: 25 loop : -3.18 (0.57), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 383 TYR 0.023 0.002 TYR B 156 PHE 0.013 0.001 PHE B 429 TRP 0.009 0.001 TRP B 173 HIS 0.007 0.002 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 2692) covalent geometry : angle 0.53375 ( 3664) SS BOND : bond 0.00175 ( 5) SS BOND : angle 0.73235 ( 10) hydrogen bonds : bond 0.04251 ( 180) hydrogen bonds : angle 3.95219 ( 537) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 49 time to evaluate : 0.085 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 51 average time/residue: 0.0377 time to fit residues: 2.4832 Evaluate side-chains 56 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 173 TRP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 400 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 28 optimal weight: 0.1980 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 18 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 152 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.166682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.133886 restraints weight = 3903.587| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.59 r_work: 0.3593 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2697 Z= 0.124 Angle : 0.514 6.279 3674 Z= 0.273 Chirality : 0.042 0.133 429 Planarity : 0.005 0.047 443 Dihedral : 3.772 16.004 353 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.15 % Allowed : 16.49 % Favored : 78.35 % 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: 1.90 (0.48), residues: 317 helix: 2.81 (0.34), residues: 215 sheet: -0.04 (1.07), residues: 25 loop : -3.13 (0.58), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 383 TYR 0.022 0.002 TYR B 156 PHE 0.010 0.001 PHE B 429 TRP 0.008 0.001 TRP B 173 HIS 0.007 0.002 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 2692) covalent geometry : angle 0.51390 ( 3664) SS BOND : bond 0.00150 ( 5) SS BOND : angle 0.59303 ( 10) hydrogen bonds : bond 0.03993 ( 180) hydrogen bonds : angle 3.82291 ( 537) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 52 time to evaluate : 0.075 Fit side-chains REVERT: B 131 PHE cc_start: 0.7480 (OUTLIER) cc_final: 0.6937 (m-80) outliers start: 15 outliers final: 11 residues processed: 55 average time/residue: 0.0396 time to fit residues: 2.8364 Evaluate side-chains 63 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 51 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 173 TRP Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 400 VAL Chi-restraints excluded: chain B residue 436 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 1 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 GLN B 157 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.157424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.124312 restraints weight = 3914.787| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.53 r_work: 0.3468 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.053 2697 Z= 0.273 Angle : 0.678 6.447 3674 Z= 0.363 Chirality : 0.048 0.142 429 Planarity : 0.006 0.053 443 Dihedral : 4.540 24.179 353 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.05 % Favored : 94.95 % Rotamer: Outliers : 5.15 % Allowed : 18.90 % Favored : 75.95 % 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: 1.02 (0.47), residues: 317 helix: 2.10 (0.34), residues: 216 sheet: -0.24 (1.02), residues: 25 loop : -3.44 (0.56), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 383 TYR 0.027 0.003 TYR B 441 PHE 0.026 0.002 PHE B 429 TRP 0.008 0.002 TRP B 210 HIS 0.012 0.003 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00662 ( 2692) covalent geometry : angle 0.67689 ( 3664) SS BOND : bond 0.00365 ( 5) SS BOND : angle 1.01862 ( 10) hydrogen bonds : bond 0.05709 ( 180) hydrogen bonds : angle 4.40283 ( 537) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.076 Fit side-chains REVERT: B 75 THR cc_start: 0.8525 (t) cc_final: 0.8012 (p) REVERT: B 441 TYR cc_start: 0.7581 (m-10) cc_final: 0.7123 (m-10) outliers start: 15 outliers final: 11 residues processed: 53 average time/residue: 0.0583 time to fit residues: 3.7831 Evaluate side-chains 57 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 TRP Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 400 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN B 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.163018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130288 restraints weight = 3904.691| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.55 r_work: 0.3540 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2697 Z= 0.130 Angle : 0.544 6.333 3674 Z= 0.290 Chirality : 0.043 0.129 429 Planarity : 0.005 0.048 443 Dihedral : 4.059 18.687 353 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 2.84 % Favored : 96.85 % Rotamer: Outliers : 4.47 % Allowed : 21.31 % Favored : 74.23 % 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: 1.57 (0.48), residues: 317 helix: 2.57 (0.34), residues: 214 sheet: -0.27 (1.03), residues: 25 loop : -3.17 (0.58), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 383 TYR 0.017 0.002 TYR B 113 PHE 0.007 0.001 PHE B 104 TRP 0.004 0.001 TRP B 173 HIS 0.009 0.002 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 2692) covalent geometry : angle 0.54313 ( 3664) SS BOND : bond 0.00153 ( 5) SS BOND : angle 0.67333 ( 10) hydrogen bonds : bond 0.04283 ( 180) hydrogen bonds : angle 3.99198 ( 537) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.085 Fit side-chains outliers start: 13 outliers final: 11 residues processed: 54 average time/residue: 0.0411 time to fit residues: 2.8962 Evaluate side-chains 57 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 88 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 433 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 13 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.162767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.130101 restraints weight = 3877.874| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.55 r_work: 0.3537 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2697 Z= 0.141 Angle : 0.556 6.347 3674 Z= 0.293 Chirality : 0.043 0.130 429 Planarity : 0.005 0.048 443 Dihedral : 4.028 18.913 353 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.79 % Favored : 95.90 % Rotamer: Outliers : 4.12 % Allowed : 22.34 % Favored : 73.54 % 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: 1.63 (0.48), residues: 317 helix: 2.62 (0.34), residues: 214 sheet: -0.18 (1.02), residues: 25 loop : -3.18 (0.58), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 383 TYR 0.017 0.002 TYR B 113 PHE 0.009 0.001 PHE B 429 TRP 0.005 0.001 TRP B 120 HIS 0.008 0.002 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 2692) covalent geometry : angle 0.55495 ( 3664) SS BOND : bond 0.00213 ( 5) SS BOND : angle 0.81741 ( 10) hydrogen bonds : bond 0.04361 ( 180) hydrogen bonds : angle 3.94306 ( 537) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.109 Fit side-chains REVERT: B 441 TYR cc_start: 0.7218 (m-10) cc_final: 0.6926 (m-10) outliers start: 12 outliers final: 11 residues processed: 52 average time/residue: 0.0439 time to fit residues: 3.0199 Evaluate side-chains 58 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 108 ASN Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 227 MET Chi-restraints excluded: chain B residue 433 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 28 optimal weight: 0.0770 chunk 20 optimal weight: 0.4980 chunk 1 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 30 optimal weight: 0.4980 chunk 13 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.164774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.131825 restraints weight = 3954.756| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 2.59 r_work: 0.3556 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7464 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2697 Z= 0.125 Angle : 0.539 6.340 3674 Z= 0.283 Chirality : 0.043 0.129 429 Planarity : 0.005 0.048 443 Dihedral : 3.927 17.820 353 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.47 % Favored : 96.21 % Rotamer: Outliers : 4.47 % Allowed : 21.99 % Favored : 73.54 % 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: 1.78 (0.48), residues: 317 helix: 2.72 (0.34), residues: 214 sheet: -0.05 (1.04), residues: 25 loop : -3.12 (0.58), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 383 TYR 0.017 0.002 TYR B 147 PHE 0.010 0.001 PHE B 104 TRP 0.003 0.001 TRP B 428 HIS 0.007 0.002 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 2692) covalent geometry : angle 0.53849 ( 3664) SS BOND : bond 0.00106 ( 5) SS BOND : angle 0.66787 ( 10) hydrogen bonds : bond 0.04104 ( 180) hydrogen bonds : angle 3.84819 ( 537) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.097 Fit side-chains REVERT: B 131 PHE cc_start: 0.7592 (OUTLIER) cc_final: 0.7276 (m-80) outliers start: 13 outliers final: 11 residues processed: 51 average time/residue: 0.0458 time to fit residues: 3.0457 Evaluate side-chains 59 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 111 MET Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 173 TRP Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 433 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 23 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 0 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.164553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.131342 restraints weight = 3958.875| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.59 r_work: 0.3549 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2697 Z= 0.130 Angle : 0.541 6.343 3674 Z= 0.284 Chirality : 0.043 0.129 429 Planarity : 0.005 0.048 443 Dihedral : 3.919 17.559 353 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.15 % Favored : 96.53 % Rotamer: Outliers : 5.15 % Allowed : 21.99 % Favored : 72.85 % 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: 1.80 (0.48), residues: 317 helix: 2.71 (0.34), residues: 214 sheet: 0.09 (1.05), residues: 25 loop : -3.10 (0.60), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 383 TYR 0.017 0.002 TYR B 147 PHE 0.007 0.001 PHE B 429 TRP 0.003 0.001 TRP B 428 HIS 0.007 0.002 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 2692) covalent geometry : angle 0.54068 ( 3664) SS BOND : bond 0.00109 ( 5) SS BOND : angle 0.63692 ( 10) hydrogen bonds : bond 0.04137 ( 180) hydrogen bonds : angle 3.82327 ( 537) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.088 Fit side-chains REVERT: B 131 PHE cc_start: 0.7600 (OUTLIER) cc_final: 0.7292 (m-80) outliers start: 15 outliers final: 11 residues processed: 53 average time/residue: 0.0436 time to fit residues: 2.9823 Evaluate side-chains 59 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 ILE Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 173 TRP Chi-restraints excluded: chain B residue 175 ILE Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 433 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 30 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 chunk 31 optimal weight: 0.8980 chunk 2 optimal weight: 9.9990 chunk 23 optimal weight: 0.4980 chunk 28 optimal weight: 0.0000 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 0.3980 chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 overall best weight: 0.3122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 108 ASN ** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 433 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.167462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.135041 restraints weight = 3962.240| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.61 r_work: 0.3597 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7408 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2697 Z= 0.117 Angle : 0.530 6.317 3674 Z= 0.278 Chirality : 0.042 0.129 429 Planarity : 0.005 0.047 443 Dihedral : 3.770 15.302 353 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.15 % Favored : 96.53 % Rotamer: Outliers : 4.12 % Allowed : 23.71 % Favored : 72.16 % 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: 1.96 (0.49), residues: 317 helix: 2.82 (0.34), residues: 214 sheet: 0.12 (1.06), residues: 25 loop : -2.99 (0.62), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 383 TYR 0.017 0.002 TYR B 147 PHE 0.006 0.001 PHE B 181 TRP 0.005 0.001 TRP B 120 HIS 0.007 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 2692) covalent geometry : angle 0.52935 ( 3664) SS BOND : bond 0.00098 ( 5) SS BOND : angle 0.60870 ( 10) hydrogen bonds : bond 0.03691 ( 180) hydrogen bonds : angle 3.71929 ( 537) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 634 Ramachandran restraints generated. 317 Oldfield, 0 Emsley, 317 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.101 Fit side-chains REVERT: B 131 PHE cc_start: 0.7529 (OUTLIER) cc_final: 0.7303 (m-80) outliers start: 12 outliers final: 8 residues processed: 50 average time/residue: 0.0429 time to fit residues: 2.8220 Evaluate side-chains 52 residues out of total 291 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 ILE Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 131 PHE Chi-restraints excluded: chain B residue 159 LYS Chi-restraints excluded: chain B residue 169 ILE Chi-restraints excluded: chain B residue 173 TRP Chi-restraints excluded: chain B residue 433 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 6 optimal weight: 0.0980 chunk 13 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.1980 chunk 27 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.4093 r_free = 0.4093 target = 0.164984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.132682 restraints weight = 3938.306| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.59 r_work: 0.3567 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7452 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2697 Z= 0.138 Angle : 0.544 6.366 3674 Z= 0.287 Chirality : 0.043 0.130 429 Planarity : 0.005 0.048 443 Dihedral : 3.834 17.006 353 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.32 % Allowed : 3.15 % Favored : 96.53 % Rotamer: Outliers : 4.12 % Allowed : 24.05 % Favored : 71.82 % 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: 1.91 (0.48), residues: 317 helix: 2.75 (0.34), residues: 214 sheet: 0.23 (1.08), residues: 25 loop : -2.95 (0.62), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 383 TYR 0.018 0.002 TYR B 147 PHE 0.008 0.001 PHE B 429 TRP 0.008 0.001 TRP B 120 HIS 0.006 0.001 HIS B 138 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 2692) covalent geometry : angle 0.54416 ( 3664) SS BOND : bond 0.00124 ( 5) SS BOND : angle 0.62707 ( 10) hydrogen bonds : bond 0.03999 ( 180) hydrogen bonds : angle 3.76514 ( 537) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 745.90 seconds wall clock time: 13 minutes 29.99 seconds (809.99 seconds total)