Starting phenix.real_space_refine on Wed Jul 1 21:20:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yw6_39624/07_2026/8yw6_39624.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yw6_39624/07_2026/8yw6_39624.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yw6_39624/07_2026/8yw6_39624.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yw6_39624/07_2026/8yw6_39624.map" model { file = "/net/cci-nas-00/data/ceres_data/8yw6_39624/07_2026/8yw6_39624.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yw6_39624/07_2026/8yw6_39624.cif" } resolution = 3.18 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= 0.001 sd= 0.024 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 3 5.49 5 S 17 5.16 5 C 1783 2.51 5 N 460 2.21 5 O 484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2747 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1000 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1000 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 118} Chain: "C" Number of atoms: 879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 879 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "A" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 745 Classifications: {'peptide': 93} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 88} Chain: "B" Number of atoms: 123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 123 Unusual residues: {'CDL': 1, 'PC8': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 11 Time building chain proxies: 0.85, per 1000 atoms: 0.31 Number of scatterers: 2747 At special positions: 0 Unit cell: (78.66, 79.23, 91.77, 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 17 16.00 P 3 15.00 O 484 8.00 N 460 7.00 C 1783 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 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: 0.25 Conformation dependent library (CDL) restraints added in 98.1 milliseconds 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 614 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 3 sheets defined 61.9% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.08 Creating SS restraints... Processing helix chain 'B' and resid 3 through 24 Processing helix chain 'B' and resid 28 through 33 Processing helix chain 'B' and resid 40 through 56 removed outlier: 3.708A pdb=" N TRP B 44 " --> pdb=" O THR B 40 " (cutoff:3.500A) Proline residue: B 46 - end of helix Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 68 through 86 Processing helix chain 'B' and resid 93 through 125 Processing helix chain 'C' and resid 62 through 65 Processing helix chain 'C' and resid 87 through 91 Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 24 through 34 Proline residue: A 30 - end of helix removed outlier: 3.585A pdb=" N TRP A 34 " --> pdb=" O PRO A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 43 Processing helix chain 'A' and resid 44 through 46 No H-bonds generated for 'chain 'A' and resid 44 through 46' Processing helix chain 'A' and resid 47 through 51 Processing helix chain 'A' and resid 52 through 73 Processing helix chain 'A' and resid 77 through 108 Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.321A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG C 38 " --> pdb=" O TRP C 47 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N TRP C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 13 removed outlier: 6.321A pdb=" N GLY C 10 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 7.754A pdb=" N SER C 114 " --> pdb=" O GLY C 10 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N VAL C 12 " --> pdb=" O SER C 114 " (cutoff:3.500A) 179 hydrogen bonds defined for protein. 489 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: 0.39 Time building geometry restraints manager: 0.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 409 1.30 - 1.43: 777 1.43 - 1.56: 1581 1.56 - 1.68: 19 1.68 - 1.81: 28 Bond restraints: 2814 Sorted by residual: bond pdb=" CB5 CDL B 202 " pdb=" OB6 CDL B 202 " ideal model delta sigma weight residual 1.334 1.440 -0.106 2.00e-02 2.50e+03 2.78e+01 bond pdb=" CA5 CDL B 202 " pdb=" OA6 CDL B 202 " ideal model delta sigma weight residual 1.333 1.438 -0.105 2.00e-02 2.50e+03 2.73e+01 bond pdb=" CA7 CDL B 202 " pdb=" OA8 CDL B 202 " ideal model delta sigma weight residual 1.331 1.433 -0.102 2.00e-02 2.50e+03 2.62e+01 bond pdb=" CB7 CDL B 202 " pdb=" OB8 CDL B 202 " ideal model delta sigma weight residual 1.339 1.435 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" C60 CDL B 202 " pdb=" C61 CDL B 202 " ideal model delta sigma weight residual 1.527 1.610 -0.083 2.00e-02 2.50e+03 1.70e+01 ... (remaining 2809 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.23: 3717 3.23 - 6.46: 58 6.46 - 9.69: 6 9.69 - 12.93: 3 12.93 - 16.16: 3 Bond angle restraints: 3787 Sorted by residual: angle pdb=" O3 PC8 B 201 " pdb=" P1 PC8 B 201 " pdb=" O4 PC8 B 201 " ideal model delta sigma weight residual 93.28 109.44 -16.16 3.00e+00 1.11e-01 2.90e+01 angle pdb=" OA3 CDL B 202 " pdb=" PA1 CDL B 202 " pdb=" OA4 CDL B 202 " ideal model delta sigma weight residual 121.92 108.08 13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" CA ARG B 62 " pdb=" C ARG B 62 " pdb=" N PRO B 63 " ideal model delta sigma weight residual 117.79 122.61 -4.82 1.08e+00 8.57e-01 1.99e+01 angle pdb=" OB2 CDL B 202 " pdb=" PB2 CDL B 202 " pdb=" OB5 CDL B 202 " ideal model delta sigma weight residual 96.70 109.78 -13.08 3.00e+00 1.11e-01 1.90e+01 angle pdb=" N GLY C 55 " pdb=" CA GLY C 55 " pdb=" C GLY C 55 " ideal model delta sigma weight residual 114.69 109.77 4.92 1.19e+00 7.06e-01 1.71e+01 ... (remaining 3782 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.93: 1636 32.93 - 65.85: 69 65.85 - 98.78: 3 98.78 - 131.71: 0 131.71 - 164.63: 1 Dihedral angle restraints: 1709 sinusoidal: 750 harmonic: 959 Sorted by residual: dihedral pdb=" O5 PC8 B 201 " pdb=" C7 PC8 B 201 " pdb=" C8 PC8 B 201 " pdb=" O7 PC8 B 201 " ideal model delta sinusoidal sigma weight residual 52.89 -142.48 -164.63 1 3.00e+01 1.11e-03 2.10e+01 dihedral pdb=" CA TYR C 35 " pdb=" C TYR C 35 " pdb=" N TRP C 36 " pdb=" CA TRP C 36 " ideal model delta harmonic sigma weight residual 180.00 164.68 15.32 0 5.00e+00 4.00e-02 9.39e+00 dihedral pdb=" CB LYS C 97 " pdb=" CG LYS C 97 " pdb=" CD LYS C 97 " pdb=" CE LYS C 97 " ideal model delta sinusoidal sigma weight residual -180.00 -124.42 -55.58 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 1706 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 285 0.052 - 0.104: 70 0.104 - 0.155: 26 0.155 - 0.207: 7 0.207 - 0.259: 4 Chirality restraints: 392 Sorted by residual: chirality pdb=" CA THR A 56 " pdb=" N THR A 56 " pdb=" C THR A 56 " pdb=" CB THR A 56 " both_signs ideal model delta sigma weight residual False 2.53 2.78 -0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA ASN A 77 " pdb=" N ASN A 77 " pdb=" C ASN A 77 " pdb=" CB ASN A 77 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA ARG B 62 " pdb=" N ARG B 62 " pdb=" C ARG B 62 " pdb=" CB ARG B 62 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 389 not shown) Planarity restraints: 464 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 76 " 0.013 2.00e-02 2.50e+03 2.60e-02 6.77e+00 pdb=" C ARG A 76 " -0.045 2.00e-02 2.50e+03 pdb=" O ARG A 76 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN A 77 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU B 24 " -0.028 5.00e-02 4.00e+02 4.23e-02 2.86e+00 pdb=" N PRO B 25 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 25 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 25 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER C 53 " 0.007 2.00e-02 2.50e+03 1.41e-02 1.98e+00 pdb=" C SER C 53 " -0.024 2.00e-02 2.50e+03 pdb=" O SER C 53 " 0.009 2.00e-02 2.50e+03 pdb=" N GLN C 54 " 0.008 2.00e-02 2.50e+03 ... (remaining 461 not shown) Histogram of nonbonded interaction distances: 2.40 - 2.90: 1003 2.90 - 3.40: 2614 3.40 - 3.90: 4765 3.90 - 4.40: 5264 4.40 - 4.90: 8613 Nonbonded interactions: 22259 Sorted by model distance: nonbonded pdb=" OD2 ASP C 73 " pdb=" NZ LYS C 76 " model vdw 2.395 3.120 nonbonded pdb=" O4 PC8 B 201 " pdb=" O7 PC8 B 201 " model vdw 2.468 2.432 nonbonded pdb=" O GLU C 31 " pdb=" OG SER C 53 " model vdw 2.547 3.040 nonbonded pdb=" OD1 ASP B 18 " pdb=" NH2 ARG B 39 " model vdw 2.555 3.120 nonbonded pdb=" C1 PC8 B 201 " pdb=" C3 PC8 B 201 " model vdw 2.609 3.088 ... (remaining 22254 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: 2.910 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.550 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 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 : 0.011 0.106 2815 Z= 0.594 Angle : 1.091 16.157 3789 Z= 0.576 Chirality : 0.061 0.259 392 Planarity : 0.004 0.042 464 Dihedral : 16.035 164.632 1092 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.74 % Allowed : 1.48 % Favored : 97.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 0.94 (0.47), residues: 327 helix: 0.65 (0.36), residues: 176 sheet: -0.31 (0.70), residues: 55 loop : 1.64 (0.73), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 97 TYR 0.008 0.000 TYR C 95 PHE 0.001 0.000 PHE A 66 TRP 0.007 0.001 TRP C 102 HIS 0.001 0.000 HIS A 26 Details of bonding type rmsd/Z covalent geometry : bond 0.01069 / 0.59 ( 2814) covalent geometry : angle 1.09079 / 0.58 ( 3787) SS BOND : bond 0.01024 / 0.54 ( 1) SS BOND : angle 0.98399 / 0.57 ( 2) hydrogen bonds : bond 0.16961 / 11.41 ( 175) hydrogen bonds : angle 6.83407 / 4.69 ( 489) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 30 time to evaluate : 0.082 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 32 average time/residue: 0.0769 time to fit residues: 2.8138 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.0170 chunk 2 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 overall best weight: 0.7618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.185942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129380 restraints weight = 2822.278| |-----------------------------------------------------------------------------| r_work (start): 0.3381 rms_B_bonded: 2.38 r_work: 0.3232 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2815 Z= 0.145 Angle : 0.511 5.652 3789 Z= 0.269 Chirality : 0.042 0.135 392 Planarity : 0.004 0.038 464 Dihedral : 16.602 172.231 492 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 5.19 % Favored : 94.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 2.56 (0.46), residues: 327 helix: 2.31 (0.38), residues: 177 sheet: 0.08 (0.70), residues: 49 loop : 1.67 (0.65), residues: 101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 62 TYR 0.016 0.002 TYR C 95 PHE 0.013 0.002 PHE A 69 TRP 0.008 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 2814) covalent geometry : angle 0.51108 / 0.27 ( 3787) SS BOND : bond 0.00327 / 0.17 ( 1) SS BOND : angle 0.76094 / 0.44 ( 2) hydrogen bonds : bond 0.03936 / 2.76 ( 175) hydrogen bonds : angle 4.44310 / 3.10 ( 489) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 21 time to evaluate : 0.058 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 0.0505 time to fit residues: 1.2995 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 19 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ASN Chi-restraints excluded: chain C residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.182794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.127058 restraints weight = 2866.688| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.32 r_work: 0.3214 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3057 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2815 Z= 0.138 Angle : 0.475 6.123 3789 Z= 0.248 Chirality : 0.041 0.134 392 Planarity : 0.004 0.034 464 Dihedral : 14.986 152.027 492 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 4.81 % Favored : 94.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 2.57 (0.46), residues: 327 helix: 2.42 (0.39), residues: 179 sheet: -0.04 (0.68), residues: 51 loop : 1.56 (0.64), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.014 0.001 TYR C 95 PHE 0.013 0.001 PHE A 69 TRP 0.009 0.001 TRP A 28 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 ( 2814) covalent geometry : angle 0.47435 / 0.25 ( 3787) SS BOND : bond 0.00345 / 0.18 ( 1) SS BOND : angle 0.74461 / 0.41 ( 2) hydrogen bonds : bond 0.03712 / 2.61 ( 175) hydrogen bonds : angle 4.07024 / 2.85 ( 489) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.054 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.0500 time to fit residues: 1.6207 Evaluate side-chains 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 24 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 74 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 4 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 13 optimal weight: 0.0020 chunk 10 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.184747 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.129701 restraints weight = 2866.526| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.33 r_work: 0.3255 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2815 Z= 0.103 Angle : 0.424 5.199 3789 Z= 0.222 Chirality : 0.039 0.127 392 Planarity : 0.004 0.034 464 Dihedral : 13.941 143.942 492 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.74 % Allowed : 5.93 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 2.87 (0.46), residues: 327 helix: 2.82 (0.39), residues: 174 sheet: -0.03 (0.66), residues: 51 loop : 1.51 (0.62), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 62 TYR 0.012 0.001 TYR C 95 PHE 0.010 0.001 PHE A 69 TRP 0.008 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.10 ( 2814) covalent geometry : angle 0.42427 / 0.22 ( 3787) SS BOND : bond 0.00182 / 0.10 ( 1) SS BOND : angle 0.67515 / 0.39 ( 2) hydrogen bonds : bond 0.03260 / 2.29 ( 175) hydrogen bonds : angle 3.71584 / 2.61 ( 489) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 25 time to evaluate : 0.061 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 26 average time/residue: 0.0562 time to fit residues: 1.7518 Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 0.0970 chunk 25 optimal weight: 0.0980 chunk 6 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 28 optimal weight: 0.4980 chunk 20 optimal weight: 3.9990 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.185372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.130129 restraints weight = 2816.717| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 2.32 r_work: 0.3262 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 2815 Z= 0.098 Angle : 0.416 5.194 3789 Z= 0.217 Chirality : 0.039 0.129 392 Planarity : 0.004 0.033 464 Dihedral : 13.246 139.188 492 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.74 % Allowed : 8.15 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 3.01 (0.46), residues: 327 helix: 2.90 (0.39), residues: 174 sheet: 0.17 (0.68), residues: 50 loop : 1.53 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.013 0.001 TYR C 95 PHE 0.010 0.001 PHE A 69 TRP 0.007 0.001 TRP B 44 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.10 ( 2814) covalent geometry : angle 0.41548 / 0.22 ( 3787) SS BOND : bond 0.00299 / 0.16 ( 1) SS BOND : angle 0.47249 / 0.27 ( 2) hydrogen bonds : bond 0.03173 / 2.22 ( 175) hydrogen bonds : angle 3.60898 / 2.54 ( 489) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 22 time to evaluate : 0.097 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 23 average time/residue: 0.0949 time to fit residues: 2.6018 Evaluate side-chains 21 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 21 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 0 optimal weight: 8.9990 chunk 30 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 3 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.182333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.126175 restraints weight = 2822.403| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.35 r_work: 0.3211 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2815 Z= 0.129 Angle : 0.449 5.506 3789 Z= 0.234 Chirality : 0.040 0.132 392 Planarity : 0.004 0.032 464 Dihedral : 13.232 138.861 492 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 2.89 (0.47), residues: 327 helix: 2.70 (0.39), residues: 175 sheet: 0.24 (0.68), residues: 50 loop : 1.59 (0.64), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.014 0.001 TYR C 95 PHE 0.014 0.001 PHE A 69 TRP 0.007 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 ( 2814) covalent geometry : angle 0.44868 / 0.23 ( 3787) SS BOND : bond 0.00278 / 0.15 ( 1) SS BOND : angle 0.67269 / 0.39 ( 2) hydrogen bonds : bond 0.03400 / 2.39 ( 175) hydrogen bonds : angle 3.72101 / 2.61 ( 489) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 23 time to evaluate : 0.056 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.0541 time to fit residues: 1.4998 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.0050 chunk 4 optimal weight: 0.4980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 2 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.184483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.129181 restraints weight = 2799.436| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.32 r_work: 0.3245 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2815 Z= 0.101 Angle : 0.420 5.166 3789 Z= 0.219 Chirality : 0.039 0.129 392 Planarity : 0.004 0.033 464 Dihedral : 12.815 137.004 492 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.37 % Allowed : 9.63 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 3.04 (0.47), residues: 327 helix: 2.86 (0.39), residues: 174 sheet: 0.36 (0.69), residues: 50 loop : 1.57 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.012 0.001 TYR C 95 PHE 0.011 0.001 PHE A 69 TRP 0.007 0.001 TRP B 50 HIS 0.003 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.10 ( 2814) covalent geometry : angle 0.41956 / 0.22 ( 3787) SS BOND : bond 0.00219 / 0.12 ( 1) SS BOND : angle 0.40530 / 0.23 ( 2) hydrogen bonds : bond 0.03178 / 2.23 ( 175) hydrogen bonds : angle 3.64048 / 2.54 ( 489) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.058 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0445 time to fit residues: 1.2357 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 4 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.182264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.126222 restraints weight = 2868.509| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.38 r_work: 0.3209 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2815 Z= 0.124 Angle : 0.444 5.353 3789 Z= 0.231 Chirality : 0.040 0.128 392 Planarity : 0.004 0.033 464 Dihedral : 12.740 136.959 492 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.37 % Allowed : 9.63 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 2.91 (0.47), residues: 327 helix: 2.70 (0.39), residues: 174 sheet: 0.45 (0.69), residues: 50 loop : 1.53 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 39 TYR 0.014 0.001 TYR C 95 PHE 0.014 0.001 PHE A 69 TRP 0.007 0.001 TRP B 44 HIS 0.005 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 ( 2814) covalent geometry : angle 0.44421 / 0.23 ( 3787) SS BOND : bond 0.00249 / 0.13 ( 1) SS BOND : angle 0.55335 / 0.32 ( 2) hydrogen bonds : bond 0.03339 / 2.35 ( 175) hydrogen bonds : angle 3.75210 / 2.62 ( 489) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.062 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 22 average time/residue: 0.0558 time to fit residues: 1.5470 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 11 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.181174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.124438 restraints weight = 2952.892| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.45 r_work: 0.3182 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.3298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2815 Z= 0.121 Angle : 0.437 5.263 3789 Z= 0.227 Chirality : 0.040 0.126 392 Planarity : 0.004 0.034 464 Dihedral : 12.430 136.958 492 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 0.37 % Allowed : 9.63 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 2.98 (0.47), residues: 327 helix: 2.78 (0.39), residues: 174 sheet: 0.51 (0.71), residues: 50 loop : 1.50 (0.65), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.013 0.001 TYR C 95 PHE 0.013 0.001 PHE A 69 TRP 0.007 0.001 TRP B 50 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 ( 2814) covalent geometry : angle 0.43699 / 0.23 ( 3787) SS BOND : bond 0.00205 / 0.11 ( 1) SS BOND : angle 0.53171 / 0.31 ( 2) hydrogen bonds : bond 0.03272 / 2.30 ( 175) hydrogen bonds : angle 3.73602 / 2.60 ( 489) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.078 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0449 time to fit residues: 1.2604 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 12 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 29 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 17 optimal weight: 0.0980 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.184478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.125618 restraints weight = 2959.511| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.49 r_work: 0.3174 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2815 Z= 0.107 Angle : 0.429 5.197 3789 Z= 0.224 Chirality : 0.039 0.128 392 Planarity : 0.004 0.034 464 Dihedral : 11.967 134.687 492 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 0.37 % Allowed : 9.63 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 3.02 (0.47), residues: 327 helix: 2.81 (0.39), residues: 174 sheet: 0.55 (0.71), residues: 50 loop : 1.50 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 62 TYR 0.013 0.001 TYR C 95 PHE 0.011 0.001 PHE A 69 TRP 0.006 0.001 TRP B 50 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 ( 2814) covalent geometry : angle 0.42940 / 0.22 ( 3787) SS BOND : bond 0.00230 / 0.12 ( 1) SS BOND : angle 0.51490 / 0.30 ( 2) hydrogen bonds : bond 0.03178 / 2.23 ( 175) hydrogen bonds : angle 3.65581 / 2.54 ( 489) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 654 Ramachandran restraints generated. 327 Oldfield, 0 Emsley, 327 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 22 time to evaluate : 0.087 Fit side-chains REVERT: A 44 MET cc_start: 0.7876 (mtt) cc_final: 0.7624 (mtt) outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 0.0525 time to fit residues: 1.4783 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 22 time to evaluate : 0.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 32 random chunks: chunk 18 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.181474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.122370 restraints weight = 2874.861| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.43 r_work: 0.3151 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.3399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2815 Z= 0.135 Angle : 0.460 5.477 3789 Z= 0.238 Chirality : 0.041 0.132 392 Planarity : 0.004 0.034 464 Dihedral : 12.260 136.631 492 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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 are not related in a simple way. whole: 2.86 (0.47), residues: 327 helix: 2.67 (0.39), residues: 174 sheet: 0.57 (0.71), residues: 50 loop : 1.40 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 62 TYR 0.014 0.001 TYR C 95 PHE 0.016 0.001 PHE A 69 TRP 0.006 0.001 TRP B 44 HIS 0.004 0.001 HIS A 84 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 ( 2814) covalent geometry : angle 0.45986 / 0.24 ( 3787) SS BOND : bond 0.00244 / 0.13 ( 1) SS BOND : angle 0.57307 / 0.34 ( 2) hydrogen bonds : bond 0.03397 / 2.39 ( 175) hydrogen bonds : angle 3.79437 / 2.64 ( 489) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 926.95 seconds wall clock time: 16 minutes 32.02 seconds (992.02 seconds total)