Starting phenix.real_space_refine on Mon Feb 10 22:04:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9j7v_61211/02_2025/9j7v_61211_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9j7v_61211/02_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_61211/02_2025/9j7v_61211.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9j7v_61211/02_2025/9j7v_61211.map" model { file = "/net/cci-nas-00/data/ceres_data/9j7v_61211/02_2025/9j7v_61211_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9j7v_61211/02_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-5592/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: 2.53, per 1000 atoms: 0.85 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: 0.87 Conformation dependent library (CDL) restraints added in 341.6 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: 0.28 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: 0.72 Time building geometry restraints manager: 0.92 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: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.070 Find NCS groups from input model: 0.040 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:2.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.410 ------------------------------------------------------------------------------- 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 : 0.292 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: 0.1941 time to fit residues: 7.9763 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 : 0.295 ------------------------------------------------------------------------------- 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 = 0.116687 restraints weight = 3847.841| |-----------------------------------------------------------------------------| 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: 0.2798 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.2798 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2819 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2819 r_free = 0.2819 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.66 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2819 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7785 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 5.893 4142 Z= 0.253 Chirality : 0.039 0.121 453 Planarity : 0.004 0.033 498 Dihedral : 13.833 119.265 481 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 : 0.285 Fit side-chains REVERT: A 22 ASN cc_start: 0.7440 (m110) cc_final: 0.7041 (m110) outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.1706 time to fit residues: 5.9527 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 : 0.310 ------------------------------------------------------------------------------- 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: 0.8980 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 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: 0.5980 chunk 10 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 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 = 0.144648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.116912 restraints weight = 3783.757| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 2.25 r_work: 0.2931 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 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 = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7788 moved from start: 0.0759 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= 0.183 Angle : 0.475 5.795 4142 Z= 0.244 Chirality : 0.039 0.121 453 Planarity : 0.004 0.034 498 Dihedral : 13.284 109.477 481 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 2.34 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: 2.01 (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 0.026 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 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 : 0.343 Fit side-chains REVERT: A 22 ASN cc_start: 0.7445 (m110) cc_final: 0.7045 (m110) outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.1705 time to fit residues: 6.0384 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 : 0.290 ------------------------------------------------------------------------------- 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: 0.8980 chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3367 r_free = 0.3367 target = 0.128015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.098938 restraints weight = 3783.887| |-----------------------------------------------------------------------------| r_work (start): 0.3022 rms_B_bonded: 2.38 r_work: 0.2905 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2929 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2929 r_free = 0.2929 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2929 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.0837 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= 0.204 Angle : 0.482 5.831 4142 Z= 0.246 Chirality : 0.039 0.121 453 Planarity : 0.004 0.034 498 Dihedral : 13.004 99.544 481 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.65 % Allowed : 12.30 % Favored : 87.06 % 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 (0.48), residues: 350 helix: 2.02 (0.34), residues: 268 sheet: None (None), residues: 0 loop : -1.23 (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 30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.328 Fit side-chains REVERT: A 22 ASN cc_start: 0.7426 (m110) cc_final: 0.6989 (m110) outliers start: 2 outliers final: 1 residues processed: 29 average time/residue: 0.1640 time to fit residues: 5.9601 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 ------------------------------------------------------------------------------- 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: 0.5980 chunk 23 optimal weight: 0.6980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 26 optimal weight: 1.9990 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 = 0.3621 r_free = 0.3621 target = 0.142603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.115426 restraints weight = 3801.721| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 2.20 r_work: 0.3169 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.58 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3155 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0909 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= 0.188 Angle : 0.477 5.775 4142 Z= 0.243 Chirality : 0.039 0.121 453 Planarity : 0.004 0.034 498 Dihedral : 12.798 88.192 481 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.32 % Allowed : 12.94 % 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: 1.97 (0.48), residues: 350 helix: 2.04 (0.34), residues: 268 sheet: None (None), residues: 0 loop : -1.20 (0.69), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 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 0.001 0.000 ARG A 281 *********************** 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 28 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 27 time to evaluate : 0.312 Fit side-chains REVERT: A 22 ASN cc_start: 0.7833 (m110) cc_final: 0.7433 (m110) outliers start: 1 outliers final: 1 residues processed: 27 average time/residue: 0.1707 time to fit residues: 5.8878 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 : 0.320 ------------------------------------------------------------------------------- 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: 0.8980 chunk 17 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 23 optimal weight: 5.9990 chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- 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 = 0.3591 r_free = 0.3591 target = 0.141487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.113835 restraints weight = 3881.503| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.24 r_work: 0.3207 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- 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 = 0.57 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 = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.0963 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= 0.153 Angle : 0.458 5.687 4142 Z= 0.234 Chirality : 0.039 0.121 453 Planarity : 0.004 0.032 498 Dihedral : 12.665 75.991 481 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: 2.09 (0.48), residues: 350 helix: 2.12 (0.34), residues: 268 sheet: None (None), residues: 0 loop : -1.13 (0.70), residues: 82 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 0.009 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 : 0.268 Fit side-chains REVERT: A 22 ASN cc_start: 0.7842 (m110) cc_final: 0.7444 (m110) outliers start: 1 outliers final: 1 residues processed: 28 average time/residue: 0.1472 time to fit residues: 5.3424 Evaluate side-chains 27 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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: 0.0970 chunk 32 optimal weight: 0.5980 chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.0020 chunk 33 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 6 optimal weight: 0.5980 chunk 14 optimal weight: 8.9990 overall best weight: 0.4386 ------------------------------------------------------------------------------- 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 = 0.3644 r_free = 0.3644 target = 0.145260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117250 restraints weight = 3904.358| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.33 r_work: 0.3209 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3209 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.1044 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= 0.142 Angle : 0.449 5.644 4142 Z= 0.229 Chirality : 0.038 0.120 453 Planarity : 0.003 0.032 498 Dihedral : 12.288 65.715 481 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 : 0.65 % Allowed : 13.59 % 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: 2.07 (0.49), residues: 350 helix: 2.07 (0.34), residues: 273 sheet: None (None), residues: 0 loop : -1.26 (0.74), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 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 : 0.325 Fit side-chains REVERT: A 22 ASN cc_start: 0.7828 (m110) cc_final: 0.7426 (m110) outliers start: 2 outliers final: 1 residues processed: 30 average time/residue: 0.1524 time to fit residues: 5.9532 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 : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 165 ASN 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: 0.8980 chunk 5 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3391 r_free = 0.3391 target = 0.130198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.100824 restraints weight = 3785.264| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 2.47 r_work: 0.3196 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3192 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3192 r_free = 0.3192 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3192 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.1078 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= 0.163 Angle : 0.458 5.699 4142 Z= 0.233 Chirality : 0.039 0.120 453 Planarity : 0.003 0.032 498 Dihedral : 11.715 68.215 481 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 : 0.65 % Allowed : 13.59 % 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: 2.02 (0.48), residues: 350 helix: 2.01 (0.33), residues: 274 sheet: None (None), residues: 0 loop : -1.18 (0.75), residues: 76 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 *********************** 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 30 residues out of total 309 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.314 Fit side-chains REVERT: A 22 ASN cc_start: 0.7668 (m110) cc_final: 0.7236 (m110) REVERT: A 281 ARG cc_start: 0.8074 (ttp80) cc_final: 0.7734 (ttp80) outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.1396 time to fit residues: 5.4048 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 ------------------------------------------------------------------------------- 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: 0.9980 chunk 21 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 overall best weight: 0.6978 ------------------------------------------------------------------------------- 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 = 0.3628 r_free = 0.3628 target = 0.144023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.116625 restraints weight = 3829.166| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.26 r_work: 0.3210 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 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 = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1095 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= 0.175 Angle : 0.465 5.741 4142 Z= 0.237 Chirality : 0.039 0.120 453 Planarity : 0.003 0.032 498 Dihedral : 11.353 69.991 481 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: 1.97 (0.48), residues: 350 helix: 1.97 (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 0.002 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 *********************** 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 : 0.317 Fit side-chains REVERT: A 22 ASN cc_start: 0.7877 (m110) cc_final: 0.7476 (m110) REVERT: A 281 ARG cc_start: 0.8284 (ttp80) cc_final: 0.8049 (ttp80) outliers start: 2 outliers final: 2 residues processed: 30 average time/residue: 0.1438 time to fit residues: 5.5714 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 : 0.324 ------------------------------------------------------------------------------- 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: 0.2980 chunk 18 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 10 optimal weight: 0.0040 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.0370 chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 0.0470 overall best weight: 0.1768 ------------------------------------------------------------------------------- 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 = 0.3635 r_free = 0.3635 target = 0.145485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.117512 restraints weight = 3752.929| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 2.33 r_work: 0.3184 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3188 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3188 r_free = 0.3188 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3189 r_free = 0.3189 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3189 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.1201 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= 0.124 Angle : 0.440 5.554 4142 Z= 0.224 Chirality : 0.038 0.120 453 Planarity : 0.003 0.032 498 Dihedral : 10.788 71.309 481 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.65 % Allowed : 13.59 % 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: 2.24 (0.49), residues: 350 helix: 2.20 (0.34), residues: 273 sheet: None (None), residues: 0 loop : -1.25 (0.75), 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 0.009 0.001 PHE A 217 TYR 0.010 0.001 TYR A 85 ARG 0.000 0.000 ARG A 170 ********************** 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 : 0.296 Fit side-chains REVERT: A 22 ASN cc_start: 0.7727 (m110) cc_final: 0.7315 (m110) outliers start: 2 outliers final: 2 residues processed: 29 average time/residue: 0.1186 time to fit residues: 4.6786 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 : 0.303 ------------------------------------------------------------------------------- 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 26 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 14 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 11 optimal weight: 0.0670 chunk 10 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 overall best weight: 0.5518 ------------------------------------------------------------------------------- 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 = 0.144192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.116365 restraints weight = 3751.037| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.31 r_work: 0.3164 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.56 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.1187 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= 0.158 Angle : 0.455 5.649 4142 Z= 0.230 Chirality : 0.038 0.120 453 Planarity : 0.003 0.031 498 Dihedral : 10.648 71.215 481 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % 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: 2.16 (0.49), residues: 350 helix: 2.15 (0.34), residues: 273 sheet: None (None), residues: 0 loop : -1.29 (0.74), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 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 85 ARG 0.001 0.000 ARG A 281 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1698.02 seconds wall clock time: 30 minutes 58.32 seconds (1858.32 seconds total)