Starting phenix.real_space_refine on Wed Sep 17 03:19:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jtm_61812/09_2025/9jtm_61812.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jtm_61812/09_2025/9jtm_61812.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jtm_61812/09_2025/9jtm_61812.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jtm_61812/09_2025/9jtm_61812.map" model { file = "/net/cci-nas-00/data/ceres_data/9jtm_61812/09_2025/9jtm_61812.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jtm_61812/09_2025/9jtm_61812.cif" } resolution = 2.9 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= 0.040 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 12 5.16 5 C 1874 2.51 5 N 442 2.21 5 O 490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 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: 2820 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2776 Classifications: {'peptide': 346} Link IDs: {'PTRANS': 14, 'TRANS': 331} Chain breaks: 1 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 44 Unusual residues: {'G6P': 1} Classifications: {'peptide': 1, 'undetermined': 1, 'water': 3} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'P5S:plan-3': 1} Unresolved non-hydrogen planarities: 4 Time building chain proxies: 1.01, per 1000 atoms: 0.36 Number of scatterers: 2820 At special positions: 0 Unit cell: (69.7, 83.3, 71.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 2 15.00 O 490 8.00 N 442 7.00 C 1874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 109 " - pdb=" SG CYS A 245 " 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: 0.37 Conformation dependent library (CDL) restraints added in 118.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 650 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 79.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 1 through 23 removed outlier: 4.473A pdb=" N VAL A 7 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU A 8 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 Processing helix chain 'A' and resid 39 through 45 Processing helix chain 'A' and resid 45 through 52 removed outlier: 3.878A pdb=" N HIS A 52 " --> pdb=" O PRO A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 80 removed outlier: 4.084A pdb=" N GLY A 58 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 60 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 91 Processing helix chain 'A' and resid 117 through 138 removed outlier: 3.582A pdb=" N MET A 121 " --> pdb=" O SER A 117 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL A 129 " --> pdb=" O GLY A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 173 Processing helix chain 'A' and resid 177 through 197 Processing helix chain 'A' and resid 205 through 231 removed outlier: 3.628A pdb=" N TYR A 209 " --> pdb=" O SER A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.594A pdb=" N LYS A 240 " --> pdb=" O TRP A 236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLN A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG A 243 " --> pdb=" O GLU A 239 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TRP A 244 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS A 245 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 251 removed outlier: 4.175A pdb=" N VAL A 251 " --> pdb=" O PRO A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 removed outlier: 3.635A pdb=" N THR A 255 " --> pdb=" O HIS A 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 256 through 276 removed outlier: 3.596A pdb=" N THR A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 279 through 283 Processing helix chain 'A' and resid 291 through 310 Processing helix chain 'A' and resid 318 through 339 removed outlier: 3.813A pdb=" N VAL A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Proline residue: A 334 - end of helix Processing helix chain 'A' and resid 340 through 349 183 hydrogen bonds defined for protein. 540 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: 0.41 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 415 1.31 - 1.44: 874 1.44 - 1.56: 1594 1.56 - 1.69: 3 1.69 - 1.82: 17 Bond restraints: 2903 Sorted by residual: bond pdb=" O6 G6P A 701 " pdb=" P G6P A 701 " ideal model delta sigma weight residual 1.722 1.628 0.094 2.00e-02 2.50e+03 2.20e+01 bond pdb=" C3 G6P A 701 " pdb=" C4 G6P A 701 " ideal model delta sigma weight residual 1.523 1.456 0.067 2.00e-02 2.50e+03 1.11e+01 bond pdb=" C2 G6P A 701 " pdb=" C3 G6P A 701 " ideal model delta sigma weight residual 1.523 1.461 0.062 2.00e-02 2.50e+03 9.54e+00 bond pdb=" N GLU A 110 " pdb=" CA GLU A 110 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.22e-02 6.72e+03 6.99e+00 bond pdb=" O15 P5S A 702 " pdb=" P12 P5S A 702 " ideal model delta sigma weight residual 1.493 1.440 0.053 2.00e-02 2.50e+03 6.93e+00 ... (remaining 2898 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.79: 3933 4.79 - 9.57: 25 9.57 - 14.36: 1 14.36 - 19.14: 0 19.14 - 23.93: 1 Bond angle restraints: 3960 Sorted by residual: angle pdb=" O13 P5S A 702 " pdb=" P12 P5S A 702 " pdb=" O15 P5S A 702 " ideal model delta sigma weight residual 121.25 97.32 23.93 3.00e+00 1.11e-01 6.36e+01 angle pdb=" CA ASP A 38 " pdb=" CB ASP A 38 " pdb=" CG ASP A 38 " ideal model delta sigma weight residual 112.60 116.37 -3.77 1.00e+00 1.00e+00 1.42e+01 angle pdb=" N ASN A 72 " pdb=" CA ASN A 72 " pdb=" CB ASN A 72 " ideal model delta sigma weight residual 110.16 115.39 -5.23 1.48e+00 4.57e-01 1.25e+01 angle pdb=" C ASN A 72 " pdb=" CA ASN A 72 " pdb=" CB ASN A 72 " ideal model delta sigma weight residual 110.85 104.85 6.00 1.70e+00 3.46e-01 1.25e+01 angle pdb=" N THR A 255 " pdb=" CA THR A 255 " pdb=" C THR A 255 " ideal model delta sigma weight residual 112.59 108.41 4.18 1.22e+00 6.72e-01 1.18e+01 ... (remaining 3955 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 1633 35.82 - 71.63: 38 71.63 - 107.45: 3 107.45 - 143.27: 3 143.27 - 179.09: 2 Dihedral angle restraints: 1679 sinusoidal: 670 harmonic: 1009 Sorted by residual: dihedral pdb=" C21 P5S A 702 " pdb=" C22 P5S A 702 " pdb=" C23 P5S A 702 " pdb=" C24 P5S A 702 " ideal model delta sinusoidal sigma weight residual -64.63 114.46 -179.09 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" C23 P5S A 702 " pdb=" C24 P5S A 702 " pdb=" C25 P5S A 702 " pdb=" C26 P5S A 702 " ideal model delta sinusoidal sigma weight residual -178.61 -21.94 -156.67 1 3.00e+01 1.11e-03 2.05e+01 dihedral pdb=" C17 P5S A 702 " pdb=" C20 P5S A 702 " pdb=" C21 P5S A 702 " pdb=" C22 P5S A 702 " ideal model delta sinusoidal sigma weight residual 71.45 -164.18 -124.37 1 3.00e+01 1.11e-03 1.67e+01 ... (remaining 1676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 420 0.089 - 0.178: 22 0.178 - 0.267: 4 0.267 - 0.356: 0 0.356 - 0.445: 2 Chirality restraints: 448 Sorted by residual: chirality pdb=" C2 G6P A 701 " pdb=" C1 G6P A 701 " pdb=" C3 G6P A 701 " pdb=" O2 G6P A 701 " both_signs ideal model delta sigma weight residual False -2.43 -1.99 -0.44 2.00e-01 2.50e+01 4.95e+00 chirality pdb=" C3 G6P A 701 " pdb=" C2 G6P A 701 " pdb=" C4 G6P A 701 " pdb=" O3 G6P A 701 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.42 2.00e-01 2.50e+01 4.32e+00 chirality pdb=" C1 G6P A 701 " pdb=" C2 G6P A 701 " pdb=" O1 G6P A 701 " pdb=" O5 G6P A 701 " both_signs ideal model delta sigma weight residual False -2.03 -2.24 0.21 2.00e-01 2.50e+01 1.06e+00 ... (remaining 445 not shown) Planarity restraints: 476 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 86 " 0.017 2.00e-02 2.50e+03 1.41e-02 4.94e+00 pdb=" CG TRP A 86 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP A 86 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 86 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 86 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 86 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 86 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 86 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 118 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.40e+00 pdb=" C GLY A 118 " -0.036 2.00e-02 2.50e+03 pdb=" O GLY A 118 " 0.013 2.00e-02 2.50e+03 pdb=" N HIS A 119 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 254 " 0.008 2.00e-02 2.50e+03 1.62e-02 2.63e+00 pdb=" C ASP A 254 " -0.028 2.00e-02 2.50e+03 pdb=" O ASP A 254 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 255 " 0.010 2.00e-02 2.50e+03 ... (remaining 473 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 960 2.85 - 3.36: 2673 3.36 - 3.87: 4442 3.87 - 4.39: 4753 4.39 - 4.90: 8936 Nonbonded interactions: 21764 Sorted by model distance: nonbonded pdb=" O LEU A 288 " pdb=" NZ LYS A 290 " model vdw 2.337 3.120 nonbonded pdb=" OG1 THR A 108 " pdb=" O LEU A 173 " model vdw 2.378 3.040 nonbonded pdb=" OE2 GLU A 239 " pdb=" NH2 ARG A 243 " model vdw 2.382 3.120 nonbonded pdb=" OD2 ASP A 90 " pdb=" NZ LYS A 240 " model vdw 2.427 3.120 nonbonded pdb=" O LEU A 288 " pdb=" OG SER A 289 " model vdw 2.432 3.040 ... (remaining 21759 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=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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.830 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:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.005 0.094 2904 Z= 0.271 Angle : 0.898 23.930 3962 Z= 0.419 Chirality : 0.054 0.445 448 Planarity : 0.004 0.033 476 Dihedral : 18.225 179.086 1026 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: 1.14 (0.49), residues: 342 helix: 2.03 (0.37), residues: 239 sheet: None (None), residues: 0 loop : -2.51 (0.55), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 281 TYR 0.010 0.001 TYR A 85 PHE 0.016 0.001 PHE A 223 TRP 0.038 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00496 ( 2903) covalent geometry : angle 0.89803 ( 3960) SS BOND : bond 0.00062 ( 1) SS BOND : angle 1.24981 ( 2) hydrogen bonds : bond 0.15947 ( 183) hydrogen bonds : angle 5.45558 ( 540) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.115 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 0.3818 time to fit residues: 12.2770 Evaluate side-chains 25 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.0570 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 0.0970 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 72 ASN A 179 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.137091 restraints weight = 3470.451| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.13 r_work: 0.3433 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.0869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2904 Z= 0.119 Angle : 0.544 7.133 3962 Z= 0.270 Chirality : 0.040 0.146 448 Planarity : 0.004 0.033 476 Dihedral : 16.986 146.545 417 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 0.66 % Allowed : 6.60 % Favored : 92.74 % 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: 1.65 (0.50), residues: 342 helix: 2.25 (0.35), residues: 253 sheet: None (None), residues: 0 loop : -2.56 (0.60), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 40 TYR 0.010 0.001 TYR A 85 PHE 0.012 0.001 PHE A 223 TRP 0.024 0.001 TRP A 86 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00235 ( 2903) covalent geometry : angle 0.54308 ( 3960) SS BOND : bond 0.00012 ( 1) SS BOND : angle 1.34491 ( 2) hydrogen bonds : bond 0.05178 ( 183) hydrogen bonds : angle 4.00018 ( 540) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.095 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 25 average time/residue: 0.5040 time to fit residues: 13.0477 Evaluate side-chains 22 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 32 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.158928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133177 restraints weight = 3539.402| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.14 r_work: 0.3346 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2904 Z= 0.131 Angle : 0.535 6.974 3962 Z= 0.270 Chirality : 0.041 0.148 448 Planarity : 0.004 0.045 476 Dihedral : 14.094 145.055 417 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.32 % Allowed : 7.26 % Favored : 91.42 % 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: 1.51 (0.49), residues: 342 helix: 2.16 (0.35), residues: 255 sheet: None (None), residues: 0 loop : -2.74 (0.59), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.009 0.001 TYR A 85 PHE 0.009 0.001 PHE A 223 TRP 0.021 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 2903) covalent geometry : angle 0.53402 ( 3960) SS BOND : bond 0.00049 ( 1) SS BOND : angle 1.49626 ( 2) hydrogen bonds : bond 0.05441 ( 183) hydrogen bonds : angle 3.89383 ( 540) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 25 time to evaluate : 0.113 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 28 average time/residue: 0.4581 time to fit residues: 13.3127 Evaluate side-chains 26 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 254 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 176 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.158183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.131655 restraints weight = 3554.497| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.23 r_work: 0.3370 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2904 Z= 0.138 Angle : 0.535 6.717 3962 Z= 0.272 Chirality : 0.041 0.149 448 Planarity : 0.005 0.048 476 Dihedral : 13.551 149.529 417 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.65 % Allowed : 8.58 % Favored : 89.77 % 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: 1.48 (0.49), residues: 342 helix: 2.11 (0.35), residues: 255 sheet: None (None), residues: 0 loop : -2.67 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.010 0.001 TYR A 85 PHE 0.010 0.001 PHE A 80 TRP 0.018 0.001 TRP A 86 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 2903) covalent geometry : angle 0.53440 ( 3960) SS BOND : bond 0.00020 ( 1) SS BOND : angle 1.50404 ( 2) hydrogen bonds : bond 0.05609 ( 183) hydrogen bonds : angle 3.88574 ( 540) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 26 time to evaluate : 0.115 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.4979 time to fit residues: 14.9642 Evaluate side-chains 28 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 254 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 17 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 0.0370 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.134743 restraints weight = 3486.838| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.20 r_work: 0.3419 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2904 Z= 0.116 Angle : 0.501 6.878 3962 Z= 0.255 Chirality : 0.040 0.149 448 Planarity : 0.004 0.048 476 Dihedral : 13.104 154.310 417 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.65 % Allowed : 10.23 % Favored : 88.12 % 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 (0.49), residues: 342 helix: 2.34 (0.35), residues: 253 sheet: None (None), residues: 0 loop : -2.40 (0.59), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.010 0.001 TYR A 85 PHE 0.006 0.001 PHE A 80 TRP 0.014 0.001 TRP A 86 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 2903) covalent geometry : angle 0.50028 ( 3960) SS BOND : bond 0.00035 ( 1) SS BOND : angle 1.43308 ( 2) hydrogen bonds : bond 0.04847 ( 183) hydrogen bonds : angle 3.71746 ( 540) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.113 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 27 average time/residue: 0.4728 time to fit residues: 13.2795 Evaluate side-chains 26 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 232 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 0 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 31 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 9 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.158591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132212 restraints weight = 3566.058| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.24 r_work: 0.3374 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2904 Z= 0.135 Angle : 0.545 8.978 3962 Z= 0.271 Chirality : 0.041 0.150 448 Planarity : 0.005 0.048 476 Dihedral : 13.091 157.819 417 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 1.98 % Allowed : 10.56 % Favored : 87.46 % 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: 1.61 (0.49), residues: 342 helix: 2.17 (0.35), residues: 255 sheet: None (None), residues: 0 loop : -2.48 (0.58), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 243 TYR 0.011 0.001 TYR A 85 PHE 0.009 0.001 PHE A 177 TRP 0.016 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 2903) covalent geometry : angle 0.54369 ( 3960) SS BOND : bond 0.00035 ( 1) SS BOND : angle 1.50270 ( 2) hydrogen bonds : bond 0.05403 ( 183) hydrogen bonds : angle 3.77433 ( 540) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 27 time to evaluate : 0.106 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 32 average time/residue: 0.4767 time to fit residues: 15.8113 Evaluate side-chains 28 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 232 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 5 optimal weight: 0.0670 chunk 28 optimal weight: 0.2980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.163940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.137711 restraints weight = 3508.624| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.22 r_work: 0.3463 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2904 Z= 0.105 Angle : 0.501 8.927 3962 Z= 0.249 Chirality : 0.039 0.148 448 Planarity : 0.004 0.049 476 Dihedral : 12.684 165.613 417 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.31 % Allowed : 10.23 % Favored : 87.46 % 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: 2.04 (0.50), residues: 342 helix: 2.47 (0.35), residues: 253 sheet: None (None), residues: 0 loop : -2.17 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 243 TYR 0.009 0.001 TYR A 85 PHE 0.005 0.001 PHE A 223 TRP 0.012 0.001 TRP A 86 HIS 0.002 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 2903) covalent geometry : angle 0.49994 ( 3960) SS BOND : bond 0.00036 ( 1) SS BOND : angle 1.32005 ( 2) hydrogen bonds : bond 0.04192 ( 183) hydrogen bonds : angle 3.58804 ( 540) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 27 time to evaluate : 0.114 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 32 average time/residue: 0.4034 time to fit residues: 13.4663 Evaluate side-chains 29 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN A 165 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.158703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133403 restraints weight = 3545.362| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.16 r_work: 0.3413 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2904 Z= 0.132 Angle : 0.554 9.515 3962 Z= 0.275 Chirality : 0.041 0.152 448 Planarity : 0.005 0.046 476 Dihedral : 12.822 168.950 417 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 1.65 % Allowed : 11.55 % Favored : 86.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.83 (0.49), residues: 342 helix: 2.29 (0.35), residues: 255 sheet: None (None), residues: 0 loop : -2.28 (0.60), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.010 0.001 TYR A 85 PHE 0.008 0.001 PHE A 177 TRP 0.016 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 2903) covalent geometry : angle 0.55267 ( 3960) SS BOND : bond 0.00053 ( 1) SS BOND : angle 1.46878 ( 2) hydrogen bonds : bond 0.05172 ( 183) hydrogen bonds : angle 3.68226 ( 540) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 25 time to evaluate : 0.081 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 29 average time/residue: 0.4538 time to fit residues: 13.6378 Evaluate side-chains 29 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 349 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 31 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 chunk 29 optimal weight: 0.1980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.160411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.134088 restraints weight = 3598.074| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.25 r_work: 0.3406 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2904 Z= 0.125 Angle : 0.543 8.975 3962 Z= 0.271 Chirality : 0.041 0.150 448 Planarity : 0.005 0.047 476 Dihedral : 12.828 177.717 417 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.99 % Allowed : 12.54 % Favored : 86.47 % 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: 1.93 (0.49), residues: 342 helix: 2.37 (0.34), residues: 253 sheet: None (None), residues: 0 loop : -2.14 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 243 TYR 0.009 0.001 TYR A 85 PHE 0.007 0.001 PHE A 309 TRP 0.014 0.001 TRP A 86 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 2903) covalent geometry : angle 0.54255 ( 3960) SS BOND : bond 0.00019 ( 1) SS BOND : angle 1.46168 ( 2) hydrogen bonds : bond 0.04982 ( 183) hydrogen bonds : angle 3.67168 ( 540) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 28 time to evaluate : 0.103 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 30 average time/residue: 0.5068 time to fit residues: 15.7145 Evaluate side-chains 29 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 29 optimal weight: 0.6980 chunk 33 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 24 optimal weight: 4.9990 chunk 8 optimal weight: 0.3980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.161343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.135989 restraints weight = 3565.488| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 2.17 r_work: 0.3417 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2904 Z= 0.115 Angle : 0.536 9.324 3962 Z= 0.265 Chirality : 0.040 0.149 448 Planarity : 0.004 0.047 476 Dihedral : 12.307 171.918 417 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 0.99 % Allowed : 12.87 % Favored : 86.14 % 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: 2.09 (0.49), residues: 342 helix: 2.47 (0.34), residues: 253 sheet: None (None), residues: 0 loop : -2.03 (0.62), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 243 TYR 0.011 0.001 TYR A 85 PHE 0.005 0.001 PHE A 177 TRP 0.013 0.001 TRP A 86 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 2903) covalent geometry : angle 0.53493 ( 3960) SS BOND : bond 0.00057 ( 1) SS BOND : angle 1.38778 ( 2) hydrogen bonds : bond 0.04571 ( 183) hydrogen bonds : angle 3.60685 ( 540) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 25 time to evaluate : 0.111 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 27 average time/residue: 0.4739 time to fit residues: 13.2856 Evaluate side-chains 26 residues out of total 303 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 24 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 LEU Chi-restraints excluded: chain A residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 6 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.158616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.133335 restraints weight = 3529.652| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 2.15 r_work: 0.3416 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2904 Z= 0.130 Angle : 0.554 9.146 3962 Z= 0.275 Chirality : 0.041 0.150 448 Planarity : 0.005 0.046 476 Dihedral : 12.116 166.086 417 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.99 % Allowed : 12.54 % Favored : 86.47 % 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: 1.97 (0.48), residues: 342 helix: 2.39 (0.34), residues: 253 sheet: None (None), residues: 0 loop : -2.11 (0.61), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 243 TYR 0.007 0.001 TYR A 85 PHE 0.008 0.001 PHE A 177 TRP 0.015 0.001 TRP A 86 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 2903) covalent geometry : angle 0.55325 ( 3960) SS BOND : bond 0.00059 ( 1) SS BOND : angle 1.50077 ( 2) hydrogen bonds : bond 0.05215 ( 183) hydrogen bonds : angle 3.68744 ( 540) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 927.66 seconds wall clock time: 16 minutes 35.19 seconds (995.19 seconds total)