Starting phenix.real_space_refine on Wed Mar 5 17:03:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7v_61211/03_2025/9j7v_61211_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7v_61211/03_2025/9j7v_61211.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9j7v_61211/03_2025/9j7v_61211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7v_61211/03_2025/9j7v_61211.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7v_61211/03_2025/9j7v_61211_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7v_61211/03_2025/9j7v_61211_neut.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.038 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 3 5.49 5 S 12 5.16 5 C 2000 2.51 5 N 449 2.21 5 O 511 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2975 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2828 Classifications: {'peptide': 352} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 335} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 147 Unusual residues: {'POV': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 269 Unresolved non-hydrogen angles: 318 Unresolved non-hydrogen dihedrals: 243 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'POV:plan-3': 5, 'POV:plan-1': 5} Unresolved non-hydrogen planarities: 33 Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" C1 POV A 401 " occ=0.75 ... (31 atoms not shown) pdb="C215 POV A 401 " occ=0.75 residue: pdb=" C1 POV A 407 " occ=0.75 ... (26 atoms not shown) pdb=" P POV A 407 " occ=0.75 residue: pdb=" C1 POV A 408 " occ=0.75 ... (26 atoms not shown) pdb="C210 POV A 408 " occ=0.75 Time building chain proxies: 2.82, per 1000 atoms: 0.95 Number of scatterers: 2975 At special positions: 0 Unit cell: (68.85, 72.25, 75.65, 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 3 15.00 O 511 8.00 N 449 7.00 C 2000 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: 0.78 Conformation dependent library (CDL) restraints added in 322.9 milliseconds 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 0 sheets defined 79.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 1 through 23 Processing helix chain 'A' and resid 26 through 37 Processing helix chain 'A' and resid 38 through 45 removed outlier: 3.922A pdb=" N ALA A 42 " --> pdb=" O ASP A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 removed outlier: 3.938A pdb=" N ILE A 49 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 80 removed outlier: 4.177A pdb=" N PHE A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 91 removed outlier: 4.924A pdb=" N LEU A 89 " --> pdb=" O TYR A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 96 removed outlier: 4.561A pdb=" N ASN A 96 " --> pdb=" O TYR A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 138 Processing helix chain 'A' and resid 145 through 173 removed outlier: 3.571A pdb=" N ARG A 170 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE A 171 " --> pdb=" O CYS A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 195 removed outlier: 3.744A pdb=" N GLY A 184 " --> pdb=" O GLN A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 230 Processing helix chain 'A' and resid 236 through 245 removed outlier: 3.847A pdb=" N LYS A 240 " --> pdb=" O TRP A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 277 Processing helix chain 'A' and resid 277 through 283 Processing helix chain 'A' and resid 291 through 310 removed outlier: 3.525A pdb=" N ARG A 295 " --> pdb=" O TRP A 291 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 306 " --> pdb=" O SER A 302 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 331 Processing helix chain 'A' and resid 331 through 349 removed outlier: 3.801A pdb=" N LEU A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER A 339 " --> pdb=" O LEU A 335 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N ILE A 341 " --> pdb=" O SER A 337 " (cutoff:3.500A) Proline residue: A 342 - end of helix 194 hydrogen bonds defined for protein. 579 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: 0.67 Time building geometry restraints manager: 0.89 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: 428 1.31 - 1.44: 910 1.44 - 1.56: 1701 1.56 - 1.69: 3 1.69 - 1.82: 17 Bond restraints: 3059 Sorted by residual: bond pdb=" O12 POV A 408 " pdb=" P POV A 408 " ideal model delta sigma weight residual 1.657 1.509 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" O12 POV A 401 " pdb=" P POV A 401 " ideal model delta sigma weight residual 1.657 1.510 0.147 2.00e-02 2.50e+03 5.43e+01 bond pdb=" O12 POV A 407 " pdb=" P POV A 407 " ideal model delta sigma weight residual 1.657 1.510 0.147 2.00e-02 2.50e+03 5.42e+01 bond pdb=" C31 POV A 407 " pdb=" O31 POV A 407 " ideal model delta sigma weight residual 1.327 1.400 -0.073 2.00e-02 2.50e+03 1.34e+01 bond pdb=" C31 POV A 401 " pdb=" O31 POV A 401 " ideal model delta sigma weight residual 1.327 1.399 -0.072 2.00e-02 2.50e+03 1.31e+01 ... (remaining 3054 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 4054 2.40 - 4.79: 45 4.79 - 7.19: 19 7.19 - 9.59: 17 9.59 - 11.99: 7 Bond angle restraints: 4142 Sorted by residual: angle pdb=" O11 POV A 401 " pdb=" P POV A 401 " pdb=" O12 POV A 401 " ideal model delta sigma weight residual 97.67 109.66 -11.99 3.00e+00 1.11e-01 1.60e+01 angle pdb=" O11 POV A 407 " pdb=" P POV A 407 " pdb=" O12 POV A 407 " ideal model delta sigma weight residual 97.67 109.62 -11.95 3.00e+00 1.11e-01 1.59e+01 angle pdb=" O13 POV A 401 " pdb=" P POV A 401 " pdb=" O14 POV A 401 " ideal model delta sigma weight residual 121.11 109.21 11.90 3.00e+00 1.11e-01 1.57e+01 angle pdb=" O11 POV A 408 " pdb=" P POV A 408 " pdb=" O12 POV A 408 " ideal model delta sigma weight residual 97.67 109.39 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O13 POV A 407 " pdb=" P POV A 407 " pdb=" O14 POV A 407 " ideal model delta sigma weight residual 121.11 109.42 11.69 3.00e+00 1.11e-01 1.52e+01 ... (remaining 4137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.01: 1685 31.01 - 62.03: 78 62.03 - 93.04: 4 93.04 - 124.05: 0 124.05 - 155.07: 1 Dihedral angle restraints: 1768 sinusoidal: 741 harmonic: 1027 Sorted by residual: dihedral pdb=" CA ILE A 78 " pdb=" C ILE A 78 " pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" C3 POV A 407 " pdb=" C31 POV A 407 " pdb=" O31 POV A 407 " pdb=" C32 POV A 407 " ideal model delta sinusoidal sigma weight residual 172.61 -32.32 -155.07 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA TYR A 85 " pdb=" C TYR A 85 " pdb=" N TRP A 86 " pdb=" CA TRP A 86 " ideal model delta harmonic sigma weight residual 180.00 163.97 16.03 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 1765 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 250 0.025 - 0.051: 119 0.051 - 0.076: 54 0.076 - 0.102: 21 0.102 - 0.127: 9 Chirality restraints: 453 Sorted by residual: chirality pdb=" CA PHE A 195 " pdb=" N PHE A 195 " pdb=" C PHE A 195 " pdb=" CB PHE A 195 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA THR A 255 " pdb=" N THR A 255 " pdb=" C THR A 255 " pdb=" CB THR A 255 " both_signs ideal model delta sigma weight residual False 2.53 2.40 0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA TYR A 85 " pdb=" N TYR A 85 " pdb=" C TYR A 85 " pdb=" CB TYR A 85 " both_signs ideal model delta sigma weight residual False 2.51 2.39 0.12 2.00e-01 2.50e+01 3.34e-01 ... (remaining 450 not shown) Planarity restraints: 498 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 86 " 0.024 2.00e-02 2.50e+03 1.87e-02 8.72e+00 pdb=" CG TRP A 86 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP A 86 " 0.019 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 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 86 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 86 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 86 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 105 " 0.019 5.00e-02 4.00e+02 2.93e-02 1.37e+00 pdb=" N PRO A 106 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 106 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 106 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 143 " -0.018 5.00e-02 4.00e+02 2.72e-02 1.19e+00 pdb=" N PRO A 144 " 0.047 5.00e-02 4.00e+02 pdb=" CA PRO A 144 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 144 " -0.015 5.00e-02 4.00e+02 ... (remaining 495 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 331 2.75 - 3.29: 2682 3.29 - 3.82: 4697 3.82 - 4.36: 5010 4.36 - 4.90: 9402 Nonbonded interactions: 22122 Sorted by model distance: nonbonded pdb=" OD2 ASP A 69 " pdb=" ND2 ASN A 264 " model vdw 2.210 3.120 nonbonded pdb=" OG SER A 34 " pdb=" NH1 ARG A 170 " model vdw 2.370 3.120 nonbonded pdb=" O SER A 200 " pdb=" OG SER A 200 " model vdw 2.452 3.040 nonbonded pdb=" O PRO A 144 " pdb=" OG1 THR A 145 " model vdw 2.498 3.040 nonbonded pdb=" OH TYR A 85 " pdb=" O GLU A 110 " model vdw 2.500 3.040 ... (remaining 22117 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=0.99 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: 0.010 Normalize map: mean=0, sd=1: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 12.150 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 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 : 0.007 0.148 3059 Z= 0.471 Angle : 0.974 11.987 4142 Z= 0.373 Chirality : 0.039 0.127 453 Planarity : 0.004 0.029 498 Dihedral : 16.846 155.067 1105 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.49), residues: 350 helix: 2.07 (0.34), residues: 271 sheet: None (None), residues: 0 loop : -1.58 (0.67), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP A 86 HIS 0.002 0.001 HIS A 179 PHE 0.010 0.001 PHE A 217 TYR 0.010 0.001 TYR A 85 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.362 Fit side-chains REVERT: A 22 ASN cc_start: 0.7827 (m110) cc_final: 0.7527 (m110) outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.2077 time to fit residues: 8.6097 Evaluate side-chains 27 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 29 optimal weight: 0.6980 chunk 26 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.144643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116689 restraints weight = 3847.809| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 2.29 r_work: 0.2928 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.0657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3059 Z= 0.188 Angle : 0.496 5.892 4142 Z= 0.253 Chirality : 0.039 0.121 453 Planarity : 0.004 0.033 498 Dihedral : 13.832 119.257 481 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.32 % Allowed : 6.47 % Favored : 93.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.48), residues: 350 helix: 2.10 (0.34), residues: 268 sheet: None (None), residues: 0 loop : -1.19 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 86 HIS 0.002 0.001 HIS A 179 PHE 0.010 0.001 PHE A 217 TYR 0.010 0.001 TYR A 127 ARG 0.001 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.321 Fit side-chains REVERT: A 22 ASN cc_start: 0.7439 (m110) cc_final: 0.7040 (m110) outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.1734 time to fit residues: 6.1103 Evaluate side-chains 28 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 15 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 3 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 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.116833 restraints weight = 3784.920| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.25 r_work: 0.2942 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3059 Z= 0.186 Angle : 0.477 5.801 4142 Z= 0.245 Chirality : 0.039 0.121 453 Planarity : 0.004 0.034 498 Dihedral : 13.282 109.251 481 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.32 % Allowed : 10.68 % Favored : 89.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.48), residues: 350 helix: 2.06 (0.34), residues: 268 sheet: None (None), residues: 0 loop : -1.19 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 86 HIS 0.002 0.001 HIS A 179 PHE 0.009 0.001 PHE A 217 TYR 0.010 0.001 TYR A 127 ARG 0.003 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.318 Fit side-chains REVERT: A 22 ASN cc_start: 0.7430 (m110) cc_final: 0.7031 (m110) outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.1655 time to fit residues: 5.8277 Evaluate side-chains 29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.138569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.110509 restraints weight = 3793.377| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 2.26 r_work: 0.3137 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3153 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3153 r_free = 0.3153 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3153 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.0834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3059 Z= 0.182 Angle : 0.470 5.775 4142 Z= 0.241 Chirality : 0.039 0.121 453 Planarity : 0.004 0.033 498 Dihedral : 12.973 100.327 481 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.65 % Allowed : 12.62 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.48), residues: 350 helix: 2.06 (0.34), residues: 268 sheet: None (None), residues: 0 loop : -1.22 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 86 HIS 0.002 0.001 HIS A 179 PHE 0.009 0.001 PHE A 217 TYR 0.010 0.001 TYR A 127 ARG 0.002 0.000 ARG A 281 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.335 Fit side-chains REVERT: A 5 MET cc_start: 0.8180 (mmm) cc_final: 0.7978 (mmp) REVERT: A 22 ASN cc_start: 0.7799 (m110) cc_final: 0.7422 (m110) outliers start: 2 outliers final: 1 residues processed: 28 average time/residue: 0.1530 time to fit residues: 5.5648 Evaluate side-chains 28 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.9980 chunk 19 optimal weight: 0.0770 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 31 optimal weight: 0.0060 chunk 26 optimal weight: 0.9980 overall best weight: 0.4954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.140067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.111898 restraints weight = 3836.898| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 2.29 r_work: 0.3212 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3059 Z= 0.149 Angle : 0.455 5.701 4142 Z= 0.232 Chirality : 0.038 0.121 453 Planarity : 0.003 0.033 498 Dihedral : 12.687 90.085 481 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.32 % Allowed : 13.27 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.48), residues: 350 helix: 2.03 (0.33), residues: 274 sheet: None (None), residues: 0 loop : -1.22 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 86 HIS 0.002 0.000 HIS A 179 PHE 0.009 0.001 PHE A 217 TYR 0.009 0.001 TYR A 85 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.280 Fit side-chains REVERT: A 5 MET cc_start: 0.8137 (mmm) cc_final: 0.7915 (mmp) REVERT: A 22 ASN cc_start: 0.7850 (m110) cc_final: 0.7484 (m110) outliers start: 1 outliers final: 1 residues processed: 29 average time/residue: 0.1423 time to fit residues: 5.3396 Evaluate side-chains 28 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 18 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 24 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.144756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.116829 restraints weight = 3940.001| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.32 r_work: 0.3177 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3165 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.60 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3165 r_free = 0.3165 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3165 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3059 Z= 0.175 Angle : 0.464 5.746 4142 Z= 0.236 Chirality : 0.039 0.121 453 Planarity : 0.003 0.033 498 Dihedral : 12.622 77.266 481 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.32 % Allowed : 13.92 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.48), residues: 350 helix: 1.98 (0.33), residues: 274 sheet: None (None), residues: 0 loop : -1.24 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 86 HIS 0.002 0.001 HIS A 179 PHE 0.008 0.001 PHE A 217 TYR 0.009 0.001 TYR A 127 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.318 Fit side-chains REVERT: A 5 MET cc_start: 0.8129 (mmm) cc_final: 0.7904 (mmp) REVERT: A 22 ASN cc_start: 0.7840 (m110) cc_final: 0.7434 (m110) outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.1483 time to fit residues: 5.4125 Evaluate side-chains 28 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 28 optimal weight: 0.1980 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 0.0670 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 14 optimal weight: 9.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.129660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.100441 restraints weight = 3824.154| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.41 r_work: 0.3180 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3184 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3184 r_free = 0.3184 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3184 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3059 Z= 0.162 Angle : 0.458 5.727 4142 Z= 0.233 Chirality : 0.039 0.121 453 Planarity : 0.003 0.033 498 Dihedral : 12.397 65.360 481 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.65 % Allowed : 13.92 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.48), residues: 350 helix: 2.01 (0.33), residues: 274 sheet: None (None), residues: 0 loop : -1.23 (0.74), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 86 HIS 0.002 0.001 HIS A 179 PHE 0.008 0.001 PHE A 217 TYR 0.009 0.001 TYR A 127 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.332 Fit side-chains REVERT: A 5 MET cc_start: 0.8060 (mmm) cc_final: 0.7846 (mmp) REVERT: A 22 ASN cc_start: 0.7770 (m110) cc_final: 0.7350 (m110) REVERT: A 281 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7810 (ttp80) outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.1441 time to fit residues: 5.6402 Evaluate side-chains 30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 332 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 10 optimal weight: 0.0060 chunk 34 optimal weight: 0.0870 chunk 17 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.2774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.144810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116645 restraints weight = 3778.764| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.33 r_work: 0.3140 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3059 Z= 0.128 Angle : 0.439 5.601 4142 Z= 0.223 Chirality : 0.038 0.120 453 Planarity : 0.003 0.032 498 Dihedral : 11.687 68.388 481 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.97 % Allowed : 13.59 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.20 (0.49), residues: 350 helix: 2.18 (0.34), residues: 273 sheet: None (None), residues: 0 loop : -1.27 (0.74), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 86 HIS 0.002 0.000 HIS A 179 PHE 0.008 0.001 PHE A 217 TYR 0.010 0.001 TYR A 85 ARG 0.000 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 26 time to evaluate : 0.298 Fit side-chains REVERT: A 5 MET cc_start: 0.8044 (mmm) cc_final: 0.7812 (mmp) REVERT: A 22 ASN cc_start: 0.7767 (m110) cc_final: 0.7358 (m110) REVERT: A 281 ARG cc_start: 0.8237 (ttp80) cc_final: 0.7929 (ttp80) outliers start: 3 outliers final: 2 residues processed: 29 average time/residue: 0.1143 time to fit residues: 4.5766 Evaluate side-chains 28 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 26 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 332 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 16 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 22 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.116581 restraints weight = 3823.860| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.22 r_work: 0.3219 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3224 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3224 r_free = 0.3224 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3224 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3059 Z= 0.187 Angle : 0.466 5.764 4142 Z= 0.237 Chirality : 0.039 0.121 453 Planarity : 0.003 0.032 498 Dihedral : 11.400 69.921 481 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.65 % Allowed : 13.92 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.48), residues: 350 helix: 2.02 (0.33), residues: 274 sheet: None (None), residues: 0 loop : -1.20 (0.75), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 86 HIS 0.003 0.001 HIS A 179 PHE 0.008 0.001 PHE A 217 TYR 0.008 0.001 TYR A 127 ARG 0.001 0.000 ARG A 83 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.310 Fit side-chains REVERT: A 5 MET cc_start: 0.8125 (mmm) cc_final: 0.7884 (mmp) REVERT: A 22 ASN cc_start: 0.7862 (m110) cc_final: 0.7457 (m110) outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.1446 time to fit residues: 5.5925 Evaluate side-chains 30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 25 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 11 optimal weight: 0.0060 chunk 32 optimal weight: 0.9990 chunk 28 optimal weight: 0.0670 overall best weight: 0.4134 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.144132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.116183 restraints weight = 3777.430| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.32 r_work: 0.3164 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3169 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3169 r_free = 0.3169 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.1147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 3059 Z= 0.138 Angle : 0.448 5.636 4142 Z= 0.228 Chirality : 0.038 0.120 453 Planarity : 0.003 0.032 498 Dihedral : 10.999 71.138 481 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.65 % Allowed : 14.24 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.13 (0.49), residues: 350 helix: 2.13 (0.34), residues: 273 sheet: None (None), residues: 0 loop : -1.31 (0.74), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 86 HIS 0.002 0.000 HIS A 179 PHE 0.008 0.001 PHE A 217 TYR 0.009 0.001 TYR A 85 ARG 0.001 0.000 ARG A 281 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 700 Ramachandran restraints generated. 350 Oldfield, 0 Emsley, 350 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.317 Fit side-chains REVERT: A 5 MET cc_start: 0.8057 (mmm) cc_final: 0.7822 (mmp) REVERT: A 22 ASN cc_start: 0.7772 (m110) cc_final: 0.7359 (m110) outliers start: 2 outliers final: 2 residues processed: 29 average time/residue: 0.1159 time to fit residues: 4.6249 Evaluate side-chains 29 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 27 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN Chi-restraints excluded: chain A residue 332 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 9 optimal weight: 0.4980 chunk 11 optimal weight: 0.3980 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 165 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.113887 restraints weight = 3759.793| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.29 r_work: 0.3158 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3143 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3143 r_free = 0.3143 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3143 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.1137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 3059 Z= 0.161 Angle : 0.457 5.694 4142 Z= 0.231 Chirality : 0.039 0.120 453 Planarity : 0.003 0.031 498 Dihedral : 10.811 71.347 481 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.65 % Allowed : 14.24 % Favored : 85.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.25 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.49), residues: 350 helix: 2.09 (0.34), residues: 273 sheet: None (None), residues: 0 loop : -1.34 (0.74), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 86 HIS 0.002 0.001 HIS A 179 PHE 0.008 0.001 PHE A 217 TYR 0.008 0.001 TYR A 85 ARG 0.001 0.000 ARG A 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1729.28 seconds wall clock time: 30 minutes 23.59 seconds (1823.59 seconds total)