Starting phenix.real_space_refine on Wed Sep 17 06:57:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfg_45545/09_2025/9cfg_45545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfg_45545/09_2025/9cfg_45545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cfg_45545/09_2025/9cfg_45545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfg_45545/09_2025/9cfg_45545.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfg_45545/09_2025/9cfg_45545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfg_45545/09_2025/9cfg_45545.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 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 S 14 5.16 5 C 2076 2.51 5 N 551 2.21 5 O 619 1.98 5 H 3140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 6400 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1740 Classifications: {'peptide': 115} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "L" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1653 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3007 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 14, 'TRANS': 179} Time building chain proxies: 1.37, per 1000 atoms: 0.21 Number of scatterers: 6400 At special positions: 0 Unit cell: (67.23, 85.49, 89.64, 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 14 16.00 O 619 8.00 N 551 7.00 C 2076 6.00 H 3140 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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: 0.50 Conformation dependent library (CDL) restraints added in 238.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 11.5% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.412A pdb=" N ILE A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.557A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.705A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.607A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 114 hydrogen bonds defined for protein. 264 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: 1.43 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3140 1.03 - 1.23: 5 1.23 - 1.42: 1470 1.42 - 1.62: 1856 1.62 - 1.82: 16 Bond restraints: 6487 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" H3 GLU H 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N GLU L 1 " pdb=" H2 GLU L 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N GLU H 1 " pdb=" H2 GLU H 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N ASN A 334 " pdb=" CA ASN A 334 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 6482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 11630 4.20 - 8.41: 25 8.41 - 12.61: 1 12.61 - 16.81: 1 16.81 - 21.01: 2 Bond angle restraints: 11659 Sorted by residual: angle pdb=" H1 GLU L 1 " pdb=" N GLU L 1 " pdb=" H2 GLU L 1 " ideal model delta sigma weight residual 109.47 88.46 21.01 3.00e+00 1.11e-01 4.91e+01 angle pdb=" H1 GLU H 1 " pdb=" N GLU H 1 " pdb=" H3 GLU H 1 " ideal model delta sigma weight residual 109.47 92.08 17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" H1 GLU L 1 " pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 109.47 123.45 -13.98 3.00e+00 1.11e-01 2.17e+01 angle pdb=" H1 GLU H 1 " pdb=" N GLU H 1 " pdb=" H2 GLU H 1 " ideal model delta sigma weight residual 109.47 120.66 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CG LYS A 386 " pdb=" CD LYS A 386 " pdb=" CE LYS A 386 " ideal model delta sigma weight residual 111.30 119.71 -8.41 2.30e+00 1.89e-01 1.34e+01 ... (remaining 11654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2774 17.98 - 35.96: 255 35.96 - 53.95: 73 53.95 - 71.93: 22 71.93 - 89.91: 4 Dihedral angle restraints: 3128 sinusoidal: 1663 harmonic: 1465 Sorted by residual: dihedral pdb=" CA LYS A 478 " pdb=" C LYS A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA LEU A 518 " pdb=" C LEU A 518 " pdb=" N HIS A 519 " pdb=" CA HIS A 519 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA PRO A 373 " pdb=" C PRO A 373 " pdb=" N PHE A 374 " pdb=" CA PHE A 374 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 260 0.028 - 0.056: 147 0.056 - 0.083: 38 0.083 - 0.111: 29 0.111 - 0.139: 13 Chirality restraints: 487 Sorted by residual: chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 484 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " 0.036 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 373 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 14 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO L 15 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 338 " -0.009 2.00e-02 2.50e+03 8.41e-03 2.12e+00 pdb=" CG PHE A 338 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 338 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 338 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 338 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 338 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 338 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 338 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 338 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 338 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 338 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 338 " 0.000 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 446 2.20 - 2.80: 12987 2.80 - 3.40: 18135 3.40 - 4.00: 24751 4.00 - 4.60: 36700 Nonbonded interactions: 93019 Sorted by model distance: nonbonded pdb=" OE1 GLU L 81 " pdb=" H GLU L 81 " model vdw 1.597 2.450 nonbonded pdb="HD22 ASN A 422 " pdb=" O ARG A 454 " model vdw 1.622 2.450 nonbonded pdb=" H ASN A 405 " pdb=" O GLY A 504 " model vdw 1.651 2.450 nonbonded pdb=" OD1 ASN A 422 " pdb=" H ARG A 454 " model vdw 1.673 2.450 nonbonded pdb=" OE1 GLN H 39 " pdb="HE21 GLN L 38 " model vdw 1.685 2.450 ... (remaining 93014 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: 4.260 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: 0.040 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.640 Find NCS groups from input model: 0.020 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:7.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.004 0.038 3353 Z= 0.167 Angle : 0.746 8.405 4566 Z= 0.387 Chirality : 0.044 0.139 487 Planarity : 0.005 0.053 594 Dihedral : 14.302 80.199 1200 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.28 % Allowed : 20.85 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.59 (0.42), residues: 411 helix: -2.21 (0.88), residues: 29 sheet: -0.29 (0.49), residues: 121 loop : -0.13 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 24 TYR 0.009 0.001 TYR L 49 PHE 0.025 0.001 PHE A 338 TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00383 ( 3347) covalent geometry : angle 0.74573 ( 4554) SS BOND : bond 0.00209 ( 6) SS BOND : angle 0.80149 ( 12) hydrogen bonds : bond 0.23736 ( 109) hydrogen bonds : angle 10.09393 ( 264) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.112 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8667 (mmmt) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.9095 time to fit residues: 34.0740 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 50 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.082106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.067075 restraints weight = 34861.764| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 4.75 r_work: 0.3552 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.1170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3353 Z= 0.155 Angle : 0.587 4.482 4566 Z= 0.301 Chirality : 0.043 0.135 487 Planarity : 0.005 0.038 594 Dihedral : 5.034 24.919 464 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 3.38 % Allowed : 17.18 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.61 (0.41), residues: 411 helix: -2.22 (0.83), residues: 29 sheet: -0.33 (0.46), residues: 130 loop : -0.11 (0.40), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 24 TYR 0.012 0.001 TYR L 49 PHE 0.011 0.001 PHE A 338 TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 505 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 3347) covalent geometry : angle 0.58712 ( 4554) SS BOND : bond 0.00319 ( 6) SS BOND : angle 0.62175 ( 12) hydrogen bonds : bond 0.04225 ( 109) hydrogen bonds : angle 6.78633 ( 264) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8659 (mmmt) outliers start: 12 outliers final: 6 residues processed: 44 average time/residue: 0.9515 time to fit residues: 43.3931 Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 410 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 26 optimal weight: 0.0570 chunk 29 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 overall best weight: 0.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.081928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.066488 restraints weight = 35426.727| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 4.92 r_work: 0.3548 rms_B_bonded: 4.95 restraints_weight: 0.5000 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3353 Z= 0.131 Angle : 0.556 4.361 4566 Z= 0.280 Chirality : 0.043 0.134 487 Planarity : 0.005 0.039 594 Dihedral : 4.846 23.012 464 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.14 % Favored : 95.62 % Rotamer: Outliers : 2.82 % Allowed : 17.46 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.42), residues: 411 helix: -2.11 (0.91), residues: 29 sheet: -0.25 (0.45), residues: 130 loop : -0.02 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 357 TYR 0.012 0.001 TYR A 369 PHE 0.007 0.001 PHE A 374 TRP 0.009 0.001 TRP A 353 HIS 0.001 0.001 HIS L 31 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3347) covalent geometry : angle 0.55524 ( 4554) SS BOND : bond 0.00266 ( 6) SS BOND : angle 0.68416 ( 12) hydrogen bonds : bond 0.03207 ( 109) hydrogen bonds : angle 6.04305 ( 264) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 35 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8959 (mtpp) cc_final: 0.8680 (mmmt) outliers start: 10 outliers final: 7 residues processed: 42 average time/residue: 0.7391 time to fit residues: 32.4297 Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 440 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 2 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.078749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.063789 restraints weight = 35564.942| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 4.63 r_work: 0.3484 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 3353 Z= 0.224 Angle : 0.590 4.509 4566 Z= 0.301 Chirality : 0.042 0.132 487 Planarity : 0.005 0.041 594 Dihedral : 4.973 19.905 462 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.11 % Favored : 94.65 % Rotamer: Outliers : 3.66 % Allowed : 17.75 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.42), residues: 411 helix: -2.30 (0.94), residues: 21 sheet: -0.35 (0.45), residues: 138 loop : -0.20 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 466 TYR 0.014 0.002 TYR A 369 PHE 0.008 0.001 PHE A 375 TRP 0.012 0.001 TRP A 353 HIS 0.002 0.001 HIS A 519 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 3347) covalent geometry : angle 0.58952 ( 4554) SS BOND : bond 0.00286 ( 6) SS BOND : angle 0.74301 ( 12) hydrogen bonds : bond 0.03335 ( 109) hydrogen bonds : angle 6.03924 ( 264) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8955 (mtpp) cc_final: 0.8685 (mmmt) outliers start: 13 outliers final: 7 residues processed: 40 average time/residue: 0.7737 time to fit residues: 32.4643 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 29 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.1980 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 25 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.080863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.065892 restraints weight = 35675.379| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 4.74 r_work: 0.3527 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3353 Z= 0.117 Angle : 0.533 4.175 4566 Z= 0.268 Chirality : 0.043 0.135 487 Planarity : 0.004 0.043 594 Dihedral : 4.668 18.013 462 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.14 % Favored : 95.62 % Rotamer: Outliers : 1.97 % Allowed : 19.15 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.42), residues: 411 helix: -2.29 (0.81), residues: 29 sheet: -0.18 (0.46), residues: 128 loop : -0.12 (0.41), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 466 TYR 0.012 0.001 TYR A 369 PHE 0.005 0.001 PHE A 375 TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 3347) covalent geometry : angle 0.53336 ( 4554) SS BOND : bond 0.00211 ( 6) SS BOND : angle 0.50245 ( 12) hydrogen bonds : bond 0.02790 ( 109) hydrogen bonds : angle 5.65044 ( 264) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9244 (mp) cc_final: 0.8870 (tt) REVERT: A 386 LYS cc_start: 0.8951 (mtpp) cc_final: 0.8683 (mmmt) outliers start: 7 outliers final: 5 residues processed: 38 average time/residue: 0.8953 time to fit residues: 35.3526 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 2 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3979 r_free = 0.3979 target = 0.079603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.064870 restraints weight = 35453.169| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 4.69 r_work: 0.3509 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3353 Z= 0.162 Angle : 0.543 4.342 4566 Z= 0.274 Chirality : 0.042 0.133 487 Planarity : 0.004 0.044 594 Dihedral : 4.690 19.310 462 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.11 % Favored : 94.65 % Rotamer: Outliers : 1.97 % Allowed : 19.44 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.47 (0.43), residues: 411 helix: -2.10 (0.99), residues: 21 sheet: -0.16 (0.45), residues: 138 loop : -0.15 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.014 0.001 TYR A 369 PHE 0.006 0.001 PHE A 375 TRP 0.011 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00353 ( 3347) covalent geometry : angle 0.54285 ( 4554) SS BOND : bond 0.00243 ( 6) SS BOND : angle 0.59747 ( 12) hydrogen bonds : bond 0.02872 ( 109) hydrogen bonds : angle 5.71563 ( 264) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 34 time to evaluate : 0.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9269 (mp) cc_final: 0.8867 (tt) REVERT: A 386 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8676 (mmmt) outliers start: 7 outliers final: 6 residues processed: 39 average time/residue: 0.9038 time to fit residues: 36.7318 Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 29 optimal weight: 2.9990 chunk 7 optimal weight: 0.0970 chunk 5 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.4007 r_free = 0.4007 target = 0.080595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.065861 restraints weight = 34993.832| |-----------------------------------------------------------------------------| r_work (start): 0.3667 rms_B_bonded: 4.71 r_work: 0.3538 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3353 Z= 0.111 Angle : 0.522 4.487 4566 Z= 0.261 Chirality : 0.042 0.134 487 Planarity : 0.004 0.045 594 Dihedral : 4.481 17.052 462 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % Rotamer: Outliers : 1.69 % Allowed : 20.00 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.42), residues: 411 helix: -2.07 (0.85), residues: 29 sheet: -0.03 (0.47), residues: 129 loop : -0.08 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.014 0.001 TYR A 369 PHE 0.018 0.001 PHE A 338 TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00254 ( 3347) covalent geometry : angle 0.52211 ( 4554) SS BOND : bond 0.00207 ( 6) SS BOND : angle 0.48972 ( 12) hydrogen bonds : bond 0.02616 ( 109) hydrogen bonds : angle 5.46143 ( 264) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 37 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9243 (mp) cc_final: 0.8839 (tt) REVERT: A 386 LYS cc_start: 0.8952 (mtpp) cc_final: 0.8682 (mmmt) outliers start: 6 outliers final: 4 residues processed: 40 average time/residue: 0.9726 time to fit residues: 40.3455 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 4.9990 chunk 16 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 1.4124 ------------------------------------------------------------------------------- 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 = 0.3973 r_free = 0.3973 target = 0.079146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.064334 restraints weight = 35416.976| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 4.67 r_work: 0.3494 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3353 Z= 0.184 Angle : 0.564 5.210 4566 Z= 0.285 Chirality : 0.042 0.134 487 Planarity : 0.004 0.043 594 Dihedral : 4.689 20.086 462 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.35 % Favored : 94.40 % Rotamer: Outliers : 1.69 % Allowed : 20.28 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.42), residues: 411 helix: -1.72 (1.05), residues: 21 sheet: -0.10 (0.45), residues: 135 loop : -0.20 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 357 TYR 0.015 0.001 TYR A 369 PHE 0.006 0.001 PHE A 497 TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 3347) covalent geometry : angle 0.56363 ( 4554) SS BOND : bond 0.00251 ( 6) SS BOND : angle 0.59247 ( 12) hydrogen bonds : bond 0.02907 ( 109) hydrogen bonds : angle 5.61833 ( 264) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9230 (mp) cc_final: 0.8832 (tt) REVERT: A 386 LYS cc_start: 0.8948 (mtpp) cc_final: 0.8683 (mmmt) outliers start: 6 outliers final: 4 residues processed: 35 average time/residue: 1.0144 time to fit residues: 36.7361 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 31 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 73 ASN Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.080396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.065570 restraints weight = 35557.769| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 4.74 r_work: 0.3525 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3353 Z= 0.125 Angle : 0.557 9.114 4566 Z= 0.277 Chirality : 0.042 0.136 487 Planarity : 0.004 0.043 594 Dihedral : 4.495 18.052 462 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.24 % Allowed : 3.89 % Favored : 95.86 % Rotamer: Outliers : 1.13 % Allowed : 21.41 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.42), residues: 411 helix: -1.88 (0.87), residues: 29 sheet: -0.03 (0.47), residues: 128 loop : -0.21 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.014 0.001 TYR A 369 PHE 0.004 0.001 PHE A 375 TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 3347) covalent geometry : angle 0.55691 ( 4554) SS BOND : bond 0.00216 ( 6) SS BOND : angle 0.50689 ( 12) hydrogen bonds : bond 0.02624 ( 109) hydrogen bonds : angle 5.41294 ( 264) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 35 time to evaluate : 0.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9243 (mp) cc_final: 0.8822 (tt) REVERT: A 386 LYS cc_start: 0.8963 (mtpp) cc_final: 0.8695 (mmmt) outliers start: 4 outliers final: 4 residues processed: 37 average time/residue: 0.9696 time to fit residues: 37.2611 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 33 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 12 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- 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 = 0.3967 r_free = 0.3967 target = 0.078913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.064156 restraints weight = 35391.180| |-----------------------------------------------------------------------------| r_work (start): 0.3620 rms_B_bonded: 4.67 r_work: 0.3491 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3353 Z= 0.194 Angle : 0.582 7.482 4566 Z= 0.293 Chirality : 0.042 0.134 487 Planarity : 0.004 0.043 594 Dihedral : 4.719 21.621 462 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.33 % Favored : 93.43 % Rotamer: Outliers : 1.41 % Allowed : 20.85 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.52 (0.42), residues: 411 helix: -1.68 (1.08), residues: 21 sheet: -0.09 (0.45), residues: 135 loop : -0.29 (0.41), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 91 TYR 0.016 0.002 TYR A 369 PHE 0.006 0.001 PHE A 375 TRP 0.011 0.001 TRP A 353 HIS 0.004 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 3347) covalent geometry : angle 0.58228 ( 4554) SS BOND : bond 0.00252 ( 6) SS BOND : angle 0.58104 ( 12) hydrogen bonds : bond 0.02927 ( 109) hydrogen bonds : angle 5.68981 ( 264) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 33 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9217 (mp) cc_final: 0.8817 (tt) REVERT: A 386 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8685 (mmmt) REVERT: A 424 LYS cc_start: 0.7890 (tptt) cc_final: 0.7649 (tptt) outliers start: 5 outliers final: 4 residues processed: 35 average time/residue: 0.8558 time to fit residues: 31.2265 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 32 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 0.0670 overall best weight: 0.6320 ------------------------------------------------------------------------------- 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 = 0.4003 r_free = 0.4003 target = 0.080384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.065419 restraints weight = 35248.334| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 4.77 r_work: 0.3524 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3353 Z= 0.118 Angle : 0.551 6.765 4566 Z= 0.276 Chirality : 0.043 0.136 487 Planarity : 0.004 0.043 594 Dihedral : 4.503 18.533 462 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 1.13 % Allowed : 21.41 % Favored : 77.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.50 (0.42), residues: 411 helix: -1.93 (0.88), residues: 29 sheet: 0.03 (0.47), residues: 128 loop : -0.25 (0.40), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 61 TYR 0.014 0.001 TYR A 369 PHE 0.006 0.001 PHE A 392 TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 3347) covalent geometry : angle 0.55137 ( 4554) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.49170 ( 12) hydrogen bonds : bond 0.02601 ( 109) hydrogen bonds : angle 5.43576 ( 264) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2879.25 seconds wall clock time: 49 minutes 32.57 seconds (2972.57 seconds total)