Starting phenix.real_space_refine on Wed Jul 23 11:16:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8esb_28574/07_2025/8esb_28574.cif Found real_map, /net/cci-nas-00/data/ceres_data/8esb_28574/07_2025/8esb_28574.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8esb_28574/07_2025/8esb_28574.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8esb_28574/07_2025/8esb_28574.map" model { file = "/net/cci-nas-00/data/ceres_data/8esb_28574/07_2025/8esb_28574.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8esb_28574/07_2025/8esb_28574.cif" } resolution = 3.12 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= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 66 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 14 5.16 5 C 1970 2.51 5 N 563 2.21 5 O 593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 3140 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2223 Classifications: {'peptide': 273} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 260} Chain breaks: 1 Chain: "B" Number of atoms: 828 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 828 Classifications: {'peptide': 99} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 89 Classifications: {'peptide': 12} Link IDs: {'TRANS': 11} Time building chain proxies: 3.25, per 1000 atoms: 1.04 Number of scatterers: 3140 At special positions: 0 Unit cell: (84.15, 62.05, 66.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 14 16.00 O 593 8.00 N 563 7.00 C 1970 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 84 " - pdb=" SG CYS C 12 " distance=2.03 Simple disulfide: pdb=" SG CYS A 101 " - pdb=" SG CYS A 164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 203 " - pdb=" SG CYS A 259 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " 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: 0.73 Conformation dependent library (CDL) restraints added in 375.2 milliseconds 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 716 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 7 sheets defined 20.6% alpha, 41.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'A' and resid 49 through 53 removed outlier: 3.668A pdb=" N ILE A 52 " --> pdb=" O ALA A 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU A 53 " --> pdb=" O PRO A 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 49 through 53' Processing helix chain 'A' and resid 56 through 84 removed outlier: 3.763A pdb=" N TRP A 60 " --> pdb=" O GLY A 56 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR A 73 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N VAL A 76 " --> pdb=" O GLN A 72 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY A 79 " --> pdb=" O ARG A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 149 Processing helix chain 'A' and resid 151 through 162 removed outlier: 3.636A pdb=" N ALA A 158 " --> pdb=" O GLU A 154 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N TYR A 159 " --> pdb=" O GLN A 155 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 175 Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.513A pdb=" N GLN A 180 " --> pdb=" O LYS A 176 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 47 removed outlier: 6.836A pdb=" N GLY A 26 " --> pdb=" O PHE A 33 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG A 35 " --> pdb=" O ALA A 24 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA A 24 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N ASP A 37 " --> pdb=" O PHE A 22 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N PHE A 22 " --> pdb=" O ASP A 37 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN A 96 " --> pdb=" O ALA A 117 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N MET A 98 " --> pdb=" O GLN A 115 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N TYR A 113 " --> pdb=" O GLY A 100 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG A 111 " --> pdb=" O ASP A 102 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N HIS A 114 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N ALA A 125 " --> pdb=" O HIS A 114 " (cutoff:3.500A) removed outlier: 7.185A pdb=" N TYR A 116 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.543A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 202 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 201 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 186 through 191 removed outlier: 3.543A pdb=" N HIS A 188 " --> pdb=" O TRP A 204 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ARG A 202 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N LEU A 201 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N PHE A 241 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 223 removed outlier: 3.790A pdb=" N GLU A 222 " --> pdb=" O ARG A 219 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 214 " --> pdb=" O GLN A 262 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 6 through 11 Processing sheet with id=AA6, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.737A pdb=" N PHE B 62 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 55 " --> pdb=" O TYR B 63 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 44 through 45 146 hydrogen bonds defined for protein. 384 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: 0.81 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: 1.22 - 1.34: 1050 1.34 - 1.46: 765 1.46 - 1.58: 1393 1.58 - 1.69: 0 1.69 - 1.81: 20 Bond restraints: 3228 Sorted by residual: bond pdb=" CB ARG B 45 " pdb=" CG ARG B 45 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.50e+00 bond pdb=" CB PRO B 32 " pdb=" CG PRO B 32 " ideal model delta sigma weight residual 1.506 1.461 0.045 3.90e-02 6.57e+02 1.35e+00 bond pdb=" CG1 ILE B 92 " pdb=" CD1 ILE B 92 " ideal model delta sigma weight residual 1.513 1.469 0.044 3.90e-02 6.57e+02 1.28e+00 bond pdb=" CB PRO A 210 " pdb=" CG PRO A 210 " ideal model delta sigma weight residual 1.506 1.463 0.043 3.90e-02 6.57e+02 1.20e+00 bond pdb=" CB THR A 143 " pdb=" CG2 THR A 143 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.37e-01 ... (remaining 3223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.34: 4328 2.34 - 4.67: 43 4.67 - 7.01: 1 7.01 - 9.35: 1 9.35 - 11.68: 1 Bond angle restraints: 4374 Sorted by residual: angle pdb=" N VAL A 28 " pdb=" CA VAL A 28 " pdb=" C VAL A 28 " ideal model delta sigma weight residual 109.34 102.32 7.02 2.08e+00 2.31e-01 1.14e+01 angle pdb=" CA LEU A 156 " pdb=" CB LEU A 156 " pdb=" CG LEU A 156 " ideal model delta sigma weight residual 116.30 127.98 -11.68 3.50e+00 8.16e-02 1.11e+01 angle pdb=" N ASP A 29 " pdb=" CA ASP A 29 " pdb=" C ASP A 29 " ideal model delta sigma weight residual 110.80 115.73 -4.93 2.13e+00 2.20e-01 5.36e+00 angle pdb=" CB ARG B 45 " pdb=" CG ARG B 45 " pdb=" CD ARG B 45 " ideal model delta sigma weight residual 111.30 106.68 4.62 2.30e+00 1.89e-01 4.03e+00 angle pdb=" C ALA A 150 " pdb=" N HIS A 151 " pdb=" CA HIS A 151 " ideal model delta sigma weight residual 121.54 125.03 -3.49 1.91e+00 2.74e-01 3.33e+00 ... (remaining 4369 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.43: 1688 16.43 - 32.86: 167 32.86 - 49.28: 35 49.28 - 65.71: 9 65.71 - 82.14: 6 Dihedral angle restraints: 1905 sinusoidal: 789 harmonic: 1116 Sorted by residual: dihedral pdb=" CA TYR A 27 " pdb=" C TYR A 27 " pdb=" N VAL A 28 " pdb=" CA VAL A 28 " ideal model delta harmonic sigma weight residual 180.00 150.93 29.07 0 5.00e+00 4.00e-02 3.38e+01 dihedral pdb=" CA VAL A 28 " pdb=" C VAL A 28 " pdb=" N ASP A 29 " pdb=" CA ASP A 29 " ideal model delta harmonic sigma weight residual -180.00 -160.71 -19.29 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CA GLY A 162 " pdb=" C GLY A 162 " pdb=" N THR A 163 " pdb=" CA THR A 163 " ideal model delta harmonic sigma weight residual 180.00 -161.60 -18.40 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 1902 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 231 0.032 - 0.063: 147 0.063 - 0.095: 45 0.095 - 0.126: 13 0.126 - 0.158: 7 Chirality restraints: 443 Sorted by residual: chirality pdb=" CA VAL A 28 " pdb=" N VAL A 28 " pdb=" C VAL A 28 " pdb=" CB VAL A 28 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.22e-01 chirality pdb=" CA VAL A 34 " pdb=" N VAL A 34 " pdb=" C VAL A 34 " pdb=" CB VAL A 34 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA ILE B 92 " pdb=" N ILE B 92 " pdb=" C ILE B 92 " pdb=" CB ILE B 92 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.44e-01 ... (remaining 440 not shown) Planarity restraints: 571 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 274 " -0.011 2.00e-02 2.50e+03 7.29e-03 1.33e+00 pdb=" CG TRP A 274 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 TRP A 274 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP A 274 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 274 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 274 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 274 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 274 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 274 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 274 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 111 " -0.093 9.50e-02 1.11e+02 4.17e-02 1.30e+00 pdb=" NE ARG A 111 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG A 111 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A 111 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 111 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 159 " -0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C TYR A 159 " 0.019 2.00e-02 2.50e+03 pdb=" O TYR A 159 " -0.007 2.00e-02 2.50e+03 pdb=" N LEU A 160 " -0.006 2.00e-02 2.50e+03 ... (remaining 568 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 625 2.78 - 3.31: 2582 3.31 - 3.84: 4605 3.84 - 4.37: 5599 4.37 - 4.90: 10192 Nonbonded interactions: 23603 Sorted by model distance: nonbonded pdb=" OD2 ASP A 77 " pdb=" OH TYR A 116 " model vdw 2.245 3.040 nonbonded pdb=" OD1 ASP A 122 " pdb=" NE1 TRP B 60 " model vdw 2.285 3.120 nonbonded pdb=" O TRP A 107 " pdb=" NH1 ARG A 169 " model vdw 2.332 3.120 nonbonded pdb=" NH2 ARG A 14 " pdb=" O GLU A 19 " model vdw 2.364 3.120 nonbonded pdb=" O SER A 207 " pdb=" OG SER A 207 " model vdw 2.368 3.040 ... (remaining 23598 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.250 Find NCS groups from input model: 0.030 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 3232 Z= 0.232 Angle : 0.626 11.683 4382 Z= 0.330 Chirality : 0.046 0.158 443 Planarity : 0.004 0.042 571 Dihedral : 14.313 82.140 1177 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -2.63 (0.41), residues: 376 helix: -0.87 (0.61), residues: 75 sheet: -1.36 (0.44), residues: 135 loop : -2.43 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 274 HIS 0.004 0.001 HIS A 114 PHE 0.010 0.002 PHE A 33 TYR 0.016 0.001 TYR A 99 ARG 0.009 0.001 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.22906 ( 128) hydrogen bonds : angle 8.64705 ( 384) SS BOND : bond 0.00268 ( 4) SS BOND : angle 0.63094 ( 8) covalent geometry : bond 0.00572 ( 3228) covalent geometry : angle 0.62611 ( 4374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 44 time to evaluate : 0.302 Fit side-chains REVERT: A 98 MET cc_start: 0.7866 (tmm) cc_final: 0.7622 (tmm) REVERT: A 269 PRO cc_start: 0.8741 (Cg_exo) cc_final: 0.8416 (Cg_endo) REVERT: B 19 LYS cc_start: 0.8723 (mmtm) cc_final: 0.8482 (mptt) outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2204 time to fit residues: 11.3442 Evaluate side-chains 41 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 0.0870 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 33 optimal weight: 0.5980 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.089763 restraints weight = 4221.329| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.26 r_work: 0.2951 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3232 Z= 0.124 Angle : 0.537 7.292 4382 Z= 0.286 Chirality : 0.044 0.171 443 Planarity : 0.004 0.026 571 Dihedral : 4.512 27.700 429 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -1.59 (0.42), residues: 376 helix: -0.04 (0.63), residues: 75 sheet: -0.41 (0.44), residues: 134 loop : -2.07 (0.44), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 274 HIS 0.004 0.001 HIS C 8 PHE 0.008 0.001 PHE A 33 TYR 0.013 0.001 TYR A 99 ARG 0.003 0.000 ARG A 111 Details of bonding type rmsd hydrogen bonds : bond 0.04288 ( 128) hydrogen bonds : angle 5.11637 ( 384) SS BOND : bond 0.00215 ( 4) SS BOND : angle 0.73207 ( 8) covalent geometry : bond 0.00291 ( 3228) covalent geometry : angle 0.53706 ( 4374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.325 Fit side-chains REVERT: A 269 PRO cc_start: 0.9041 (Cg_exo) cc_final: 0.8829 (Cg_endo) REVERT: B 19 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8307 (mptt) outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.1951 time to fit residues: 9.5472 Evaluate side-chains 39 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.0870 chunk 9 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 20 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS 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 = 0.126009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.089034 restraints weight = 4142.132| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 3.21 r_work: 0.2944 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3232 Z= 0.128 Angle : 0.498 7.038 4382 Z= 0.266 Chirality : 0.043 0.157 443 Planarity : 0.003 0.030 571 Dihedral : 4.349 27.503 429 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.90 % Allowed : 9.34 % Favored : 89.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.79 (0.43), residues: 376 helix: 0.90 (0.65), residues: 69 sheet: 0.25 (0.45), residues: 134 loop : -1.80 (0.45), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 274 HIS 0.003 0.001 HIS A 114 PHE 0.008 0.001 PHE A 33 TYR 0.016 0.001 TYR A 99 ARG 0.002 0.000 ARG A 202 Details of bonding type rmsd hydrogen bonds : bond 0.03993 ( 128) hydrogen bonds : angle 4.71017 ( 384) SS BOND : bond 0.00225 ( 4) SS BOND : angle 0.57883 ( 8) covalent geometry : bond 0.00310 ( 3228) covalent geometry : angle 0.49747 ( 4374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.326 Fit side-chains REVERT: B 19 LYS cc_start: 0.8543 (mmtm) cc_final: 0.8325 (mptt) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.2263 time to fit residues: 11.4001 Evaluate side-chains 41 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 40 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 223 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 29 optimal weight: 0.6980 overall best weight: 1.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.123358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.087015 restraints weight = 4252.795| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.19 r_work: 0.2911 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3232 Z= 0.216 Angle : 0.561 8.516 4382 Z= 0.293 Chirality : 0.045 0.140 443 Planarity : 0.003 0.025 571 Dihedral : 4.576 28.559 429 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.51 % Allowed : 10.54 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.57 (0.44), residues: 376 helix: 1.08 (0.65), residues: 69 sheet: 0.27 (0.46), residues: 137 loop : -1.56 (0.46), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 244 HIS 0.003 0.001 HIS A 114 PHE 0.010 0.002 PHE A 33 TYR 0.020 0.002 TYR A 99 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 128) hydrogen bonds : angle 4.81226 ( 384) SS BOND : bond 0.00247 ( 4) SS BOND : angle 0.56397 ( 8) covalent geometry : bond 0.00532 ( 3228) covalent geometry : angle 0.56061 ( 4374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.346 Fit side-chains REVERT: B 19 LYS cc_start: 0.8592 (mmtm) cc_final: 0.8364 (mptt) outliers start: 5 outliers final: 4 residues processed: 43 average time/residue: 0.2593 time to fit residues: 12.9457 Evaluate side-chains 43 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 8 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.123274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.087778 restraints weight = 4271.503| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 3.17 r_work: 0.2977 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3232 Z= 0.134 Angle : 0.510 7.097 4382 Z= 0.269 Chirality : 0.043 0.160 443 Planarity : 0.003 0.027 571 Dihedral : 4.342 27.996 429 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.20 % Allowed : 11.75 % Favored : 87.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.24 (0.45), residues: 376 helix: 1.30 (0.65), residues: 69 sheet: 0.46 (0.46), residues: 137 loop : -1.31 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 167 HIS 0.002 0.001 HIS A 114 PHE 0.008 0.001 PHE A 33 TYR 0.015 0.001 TYR A 99 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03858 ( 128) hydrogen bonds : angle 4.59070 ( 384) SS BOND : bond 0.00205 ( 4) SS BOND : angle 0.46592 ( 8) covalent geometry : bond 0.00327 ( 3228) covalent geometry : angle 0.50958 ( 4374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.430 Fit side-chains REVERT: B 19 LYS cc_start: 0.8595 (mmtm) cc_final: 0.8388 (mptt) outliers start: 4 outliers final: 2 residues processed: 41 average time/residue: 0.2865 time to fit residues: 13.8662 Evaluate side-chains 41 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain C residue 8 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 23 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.085236 restraints weight = 4400.509| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.16 r_work: 0.2921 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3232 Z= 0.253 Angle : 0.576 8.077 4382 Z= 0.306 Chirality : 0.046 0.135 443 Planarity : 0.003 0.026 571 Dihedral : 4.673 28.862 429 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.51 % Allowed : 11.14 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.34 (0.44), residues: 376 helix: 1.12 (0.64), residues: 69 sheet: 0.78 (0.47), residues: 127 loop : -1.58 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 244 HIS 0.004 0.001 HIS A 114 PHE 0.011 0.002 PHE B 30 TYR 0.021 0.002 TYR A 99 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.04630 ( 128) hydrogen bonds : angle 4.83160 ( 384) SS BOND : bond 0.00255 ( 4) SS BOND : angle 0.60661 ( 8) covalent geometry : bond 0.00625 ( 3228) covalent geometry : angle 0.57613 ( 4374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.389 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.2130 time to fit residues: 10.3074 Evaluate side-chains 44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 88 SER Chi-restraints excluded: chain C residue 8 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.124831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.088463 restraints weight = 4207.981| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 3.15 r_work: 0.2949 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3232 Z= 0.163 Angle : 0.535 7.583 4382 Z= 0.280 Chirality : 0.043 0.145 443 Planarity : 0.003 0.025 571 Dihedral : 4.438 28.423 429 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.11 % Allowed : 11.45 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: -0.10 (0.44), residues: 376 helix: 1.33 (0.64), residues: 69 sheet: 0.98 (0.47), residues: 126 loop : -1.45 (0.46), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 167 HIS 0.003 0.001 HIS A 114 PHE 0.009 0.001 PHE B 30 TYR 0.017 0.001 TYR A 99 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03961 ( 128) hydrogen bonds : angle 4.61624 ( 384) SS BOND : bond 0.00200 ( 4) SS BOND : angle 0.50724 ( 8) covalent geometry : bond 0.00403 ( 3228) covalent geometry : angle 0.53546 ( 4374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.363 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 44 average time/residue: 0.2079 time to fit residues: 10.9090 Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 88 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 0.9990 chunk 12 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 0.0570 chunk 22 optimal weight: 0.6980 chunk 34 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.0370 chunk 33 optimal weight: 1.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.3454 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.127068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.090248 restraints weight = 4264.202| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 3.26 r_work: 0.2972 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 3232 Z= 0.096 Angle : 0.491 6.706 4382 Z= 0.257 Chirality : 0.042 0.158 443 Planarity : 0.003 0.025 571 Dihedral : 4.070 27.141 429 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.51 % Allowed : 12.35 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.21 (0.45), residues: 376 helix: 1.67 (0.64), residues: 69 sheet: 1.02 (0.47), residues: 131 loop : -1.23 (0.48), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 204 HIS 0.002 0.001 HIS A 93 PHE 0.008 0.001 PHE A 33 TYR 0.012 0.001 TYR A 99 ARG 0.003 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 128) hydrogen bonds : angle 4.35812 ( 384) SS BOND : bond 0.00194 ( 4) SS BOND : angle 0.40335 ( 8) covalent geometry : bond 0.00230 ( 3228) covalent geometry : angle 0.49162 ( 4374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.362 Fit side-chains REVERT: A 98 MET cc_start: 0.8454 (tmm) cc_final: 0.8181 (tmm) outliers start: 5 outliers final: 5 residues processed: 43 average time/residue: 0.2072 time to fit residues: 10.5687 Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 88 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 26 optimal weight: 0.0020 chunk 4 optimal weight: 0.3980 chunk 12 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.126584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.089545 restraints weight = 4270.299| |-----------------------------------------------------------------------------| r_work (start): 0.3134 rms_B_bonded: 3.26 r_work: 0.2960 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3232 Z= 0.116 Angle : 0.499 6.566 4382 Z= 0.262 Chirality : 0.042 0.148 443 Planarity : 0.003 0.026 571 Dihedral : 4.084 27.316 429 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.51 % Allowed : 12.65 % Favored : 85.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.24 (0.45), residues: 376 helix: 1.80 (0.64), residues: 69 sheet: 1.15 (0.47), residues: 127 loop : -1.30 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 204 HIS 0.003 0.001 HIS C 8 PHE 0.008 0.001 PHE A 33 TYR 0.014 0.001 TYR A 99 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 128) hydrogen bonds : angle 4.37733 ( 384) SS BOND : bond 0.00186 ( 4) SS BOND : angle 0.40887 ( 8) covalent geometry : bond 0.00283 ( 3228) covalent geometry : angle 0.49920 ( 4374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.353 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 44 average time/residue: 0.2056 time to fit residues: 10.7884 Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain B residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 11 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.124549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.087545 restraints weight = 4148.226| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 3.28 r_work: 0.2894 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3232 Z= 0.154 Angle : 0.525 6.918 4382 Z= 0.276 Chirality : 0.043 0.142 443 Planarity : 0.003 0.027 571 Dihedral : 4.238 27.936 429 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 1.20 % Allowed : 12.65 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.20 (0.44), residues: 376 helix: 1.74 (0.64), residues: 69 sheet: 1.15 (0.47), residues: 127 loop : -1.34 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 167 HIS 0.004 0.001 HIS C 8 PHE 0.008 0.001 PHE B 30 TYR 0.017 0.001 TYR A 99 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03748 ( 128) hydrogen bonds : angle 4.49257 ( 384) SS BOND : bond 0.00185 ( 4) SS BOND : angle 0.43553 ( 8) covalent geometry : bond 0.00380 ( 3228) covalent geometry : angle 0.52474 ( 4374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 752 Ramachandran restraints generated. 376 Oldfield, 0 Emsley, 376 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.328 Fit side-chains REVERT: A 98 MET cc_start: 0.8471 (tmm) cc_final: 0.8188 (tmm) outliers start: 4 outliers final: 4 residues processed: 44 average time/residue: 0.2010 time to fit residues: 10.5326 Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 84 CYS Chi-restraints excluded: chain A residue 121 LYS Chi-restraints excluded: chain B residue 88 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 32 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 0.0030 chunk 27 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 1 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.126591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.089687 restraints weight = 4249.567| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 3.25 r_work: 0.2964 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3232 Z= 0.108 Angle : 0.494 6.568 4382 Z= 0.259 Chirality : 0.042 0.151 443 Planarity : 0.003 0.028 571 Dihedral : 4.045 27.399 429 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.51 % Allowed : 12.35 % Favored : 86.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % 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: 0.32 (0.45), residues: 376 helix: 1.92 (0.65), residues: 69 sheet: 1.23 (0.47), residues: 127 loop : -1.31 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 204 HIS 0.003 0.001 HIS C 8 PHE 0.008 0.001 PHE A 33 TYR 0.013 0.001 TYR A 99 ARG 0.002 0.000 ARG A 108 Details of bonding type rmsd hydrogen bonds : bond 0.03352 ( 128) hydrogen bonds : angle 4.33799 ( 384) SS BOND : bond 0.00182 ( 4) SS BOND : angle 0.40314 ( 8) covalent geometry : bond 0.00263 ( 3228) covalent geometry : angle 0.49413 ( 4374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2916.83 seconds wall clock time: 52 minutes 49.42 seconds (3169.42 seconds total)