Sun 23 Dec 23:56:03 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ouw-3.2-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2ouw-3.2-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2ouw-3.2-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-parrot-mrncs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-parrot-mrncs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 23:56:07 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2ouw-3.2-parrot-mrncs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 165 and 0 Target number of residues in the AU: 165 Target solvent content: 0.6367 Checking the provided sequence file Detected sequence length: 138 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 276 Adjusted target solvent content: 0.39 Input MTZ file: 2ouw-3.2-parrot-mrncs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 182 Cell parameters: 62.683 62.683 216.710 90.000 90.000 120.000 Input sequence file: 2ouw-3.2-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2208 target number of atoms Had to go as low as 0.70 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 108.355 3.200 Wilson plot Bfac: 69.09 4672 reflections ( 99.85 % complete ) and 0 restraints for refining 2436 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3413 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3335 (Rfree = 0.000) for 2436 atoms. Found 21 (21 requested) and removed 19 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.29 3.82 Search for helices and strands: 0 residues in 0 chains, 2499 seeds are put forward NCS extension: 0 residues added, 2499 seeds are put forward Round 1: 124 peptides, 26 chains. Longest chain 8 peptides. Score 0.309 Round 2: 145 peptides, 21 chains. Longest chain 20 peptides. Score 0.562 Round 3: 152 peptides, 22 chains. Longest chain 14 peptides. Score 0.575 Round 4: 146 peptides, 23 chains. Longest chain 17 peptides. Score 0.521 Round 5: 160 peptides, 26 chains. Longest chain 20 peptides. Score 0.527 Taking the results from Round 3 Chains 23, Residues 130, Estimated correctness of the model 34.1 % 4 chains (23 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4355 restraints for refining 2016 atoms. 3791 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3004 (Rfree = 0.000) for 2016 atoms. Found 13 (18 requested) and removed 29 (9 requested) atoms. Cycle 2: After refmac, R = 0.2881 (Rfree = 0.000) for 1968 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 3: After refmac, R = 0.2797 (Rfree = 0.000) for 1957 atoms. Found 14 (17 requested) and removed 11 (8 requested) atoms. Cycle 4: After refmac, R = 0.2512 (Rfree = 0.000) for 1954 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. Cycle 5: After refmac, R = 0.2409 (Rfree = 0.000) for 1943 atoms. Found 4 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.25 3.77 Search for helices and strands: 0 residues in 0 chains, 2017 seeds are put forward NCS extension: 0 residues added, 2017 seeds are put forward Round 1: 141 peptides, 25 chains. Longest chain 15 peptides. Score 0.444 Round 2: 142 peptides, 22 chains. Longest chain 20 peptides. Score 0.523 Round 3: 155 peptides, 23 chains. Longest chain 20 peptides. Score 0.568 Round 4: 161 peptides, 22 chains. Longest chain 20 peptides. Score 0.618 Round 5: 153 peptides, 24 chains. Longest chain 14 peptides. Score 0.536 Taking the results from Round 4 Chains 23, Residues 139, Estimated correctness of the model 45.8 % 1 chains (14 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4357 restraints for refining 1966 atoms. 3780 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2858 (Rfree = 0.000) for 1966 atoms. Found 14 (17 requested) and removed 21 (8 requested) atoms. Cycle 7: After refmac, R = 0.2644 (Rfree = 0.000) for 1951 atoms. Found 14 (17 requested) and removed 10 (8 requested) atoms. Cycle 8: After refmac, R = 0.2381 (Rfree = 0.000) for 1949 atoms. Found 5 (17 requested) and removed 11 (8 requested) atoms. Cycle 9: After refmac, R = 0.3036 (Rfree = 0.000) for 1941 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 10: After refmac, R = 0.2565 (Rfree = 0.000) for 1937 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.17 3.68 Search for helices and strands: 0 residues in 0 chains, 2048 seeds are put forward NCS extension: 23 residues added (1 deleted due to clashes), 2071 seeds are put forward Round 1: 152 peptides, 29 chains. Longest chain 14 peptides. Score 0.409 Round 2: 168 peptides, 27 chains. Longest chain 18 peptides. Score 0.547 Round 3: 160 peptides, 24 chains. Longest chain 25 peptides. Score 0.571 Round 4: 161 peptides, 26 chains. Longest chain 17 peptides. Score 0.533 Round 5: 161 peptides, 24 chains. Longest chain 12 peptides. Score 0.576 Taking the results from Round 5 Chains 24, Residues 137, Estimated correctness of the model 34.4 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4382 restraints for refining 1939 atoms. 3858 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2562 (Rfree = 0.000) for 1939 atoms. Found 16 (17 requested) and removed 20 (8 requested) atoms. Cycle 12: After refmac, R = 0.2450 (Rfree = 0.000) for 1923 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 13: After refmac, R = 0.2527 (Rfree = 0.000) for 1923 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 14: After refmac, R = 0.2950 (Rfree = 0.000) for 1920 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 15: After refmac, R = 0.2600 (Rfree = 0.000) for 1917 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.16 3.67 Search for helices and strands: 0 residues in 0 chains, 2012 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 2024 seeds are put forward Round 1: 104 peptides, 21 chains. Longest chain 9 peptides. Score 0.314 Round 2: 128 peptides, 23 chains. Longest chain 12 peptides. Score 0.416 Round 3: 127 peptides, 22 chains. Longest chain 12 peptides. Score 0.436 Round 4: 112 peptides, 20 chains. Longest chain 11 peptides. Score 0.396 Round 5: 128 peptides, 21 chains. Longest chain 12 peptides. Score 0.468 Taking the results from Round 5 Chains 21, Residues 107, Estimated correctness of the model 0.7 % 2 chains (6 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4693 restraints for refining 1992 atoms. 4277 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2568 (Rfree = 0.000) for 1992 atoms. Found 12 (17 requested) and removed 11 (8 requested) atoms. Cycle 17: After refmac, R = 0.3182 (Rfree = 0.000) for 1989 atoms. Found 17 (17 requested) and removed 29 (8 requested) atoms. Cycle 18: After refmac, R = 0.2661 (Rfree = 0.000) for 1966 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 19: After refmac, R = 0.2525 (Rfree = 0.000) for 1968 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 20: After refmac, R = 0.2314 (Rfree = 0.000) for 1969 atoms. Found 15 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.19 3.70 Search for helices and strands: 0 residues in 0 chains, 2067 seeds are put forward NCS extension: 0 residues added, 2067 seeds are put forward Round 1: 88 peptides, 18 chains. Longest chain 8 peptides. Score 0.290 Round 2: 118 peptides, 21 chains. Longest chain 14 peptides. Score 0.407 Round 3: 114 peptides, 20 chains. Longest chain 12 peptides. Score 0.409 Round 4: 117 peptides, 19 chains. Longest chain 16 peptides. Score 0.454 Round 5: 118 peptides, 20 chains. Longest chain 14 peptides. Score 0.434 Taking the results from Round 4 Chains 19, Residues 98, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4494 restraints for refining 1968 atoms. 4102 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2503 (Rfree = 0.000) for 1968 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 22: After refmac, R = 0.2385 (Rfree = 0.000) for 1973 atoms. Found 9 (17 requested) and removed 12 (8 requested) atoms. Cycle 23: After refmac, R = 0.2501 (Rfree = 0.000) for 1968 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 24: After refmac, R = 0.2192 (Rfree = 0.000) for 1969 atoms. Found 7 (17 requested) and removed 11 (8 requested) atoms. Cycle 25: After refmac, R = 0.2179 (Rfree = 0.000) for 1962 atoms. Found 3 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2028 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2042 seeds are put forward Round 1: 109 peptides, 23 chains. Longest chain 10 peptides. Score 0.291 Round 2: 119 peptides, 22 chains. Longest chain 8 peptides. Score 0.386 Round 3: 128 peptides, 23 chains. Longest chain 11 peptides. Score 0.416 Round 4: 124 peptides, 23 chains. Longest chain 8 peptides. Score 0.391 Round 5: 119 peptides, 21 chains. Longest chain 10 peptides. Score 0.413 Taking the results from Round 3 Chains 23, Residues 105, Estimated correctness of the model 0.0 % 3 chains (13 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4520 restraints for refining 2016 atoms. 4090 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2400 (Rfree = 0.000) for 2016 atoms. Found 11 (18 requested) and removed 11 (9 requested) atoms. Cycle 27: After refmac, R = 0.2321 (Rfree = 0.000) for 2009 atoms. Found 11 (18 requested) and removed 16 (9 requested) atoms. Cycle 28: After refmac, R = 0.2687 (Rfree = 0.000) for 2001 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 29: After refmac, R = 0.2438 (Rfree = 0.000) for 2007 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 30: After refmac, R = 0.2428 (Rfree = 0.000) for 2009 atoms. Found 16 (18 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2119 seeds are put forward NCS extension: 0 residues added, 2119 seeds are put forward Round 1: 94 peptides, 19 chains. Longest chain 10 peptides. Score 0.302 Round 2: 108 peptides, 21 chains. Longest chain 8 peptides. Score 0.341 Round 3: 103 peptides, 18 chains. Longest chain 10 peptides. Score 0.393 Round 4: 93 peptides, 18 chains. Longest chain 8 peptides. Score 0.325 Round 5: 88 peptides, 15 chains. Longest chain 8 peptides. Score 0.380 Taking the results from Round 3 Chains 18, Residues 85, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4850 restraints for refining 2016 atoms. 4528 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2497 (Rfree = 0.000) for 2016 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 32: After refmac, R = 0.2486 (Rfree = 0.000) for 2019 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Cycle 33: After refmac, R = 0.2474 (Rfree = 0.000) for 2024 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 34: After refmac, R = 0.2440 (Rfree = 0.000) for 2029 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 35: After refmac, R = 0.2522 (Rfree = 0.000) for 2033 atoms. Found 18 (18 requested) and removed 13 (9 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.23 3.75 Search for helices and strands: 0 residues in 0 chains, 2100 seeds are put forward NCS extension: 0 residues added, 2100 seeds are put forward Round 1: 89 peptides, 19 chains. Longest chain 9 peptides. Score 0.266 Round 2: 97 peptides, 19 chains. Longest chain 9 peptides. Score 0.324 Round 3: 100 peptides, 19 chains. Longest chain 10 peptides. Score 0.344 Round 4: 106 peptides, 19 chains. Longest chain 13 peptides. Score 0.385 Round 5: 101 peptides, 19 chains. Longest chain 10 peptides. Score 0.351 Taking the results from Round 4 Chains 20, Residues 87, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4676 restraints for refining 2016 atoms. 4318 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2560 (Rfree = 0.000) for 2016 atoms. Found 18 (18 requested) and removed 12 (9 requested) atoms. Cycle 37: After refmac, R = 0.2550 (Rfree = 0.000) for 2017 atoms. Found 18 (18 requested) and removed 9 (9 requested) atoms. Cycle 38: After refmac, R = 0.2700 (Rfree = 0.000) for 2026 atoms. Found 18 (18 requested) and removed 15 (9 requested) atoms. Cycle 39: After refmac, R = 0.2544 (Rfree = 0.000) for 2025 atoms. Found 18 (18 requested) and removed 11 (9 requested) atoms. Cycle 40: After refmac, R = 0.2244 (Rfree = 0.000) for 2031 atoms. Found 2 (18 requested) and removed 10 (9 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.24 3.76 Search for helices and strands: 0 residues in 0 chains, 2075 seeds are put forward NCS extension: 0 residues added, 2075 seeds are put forward Round 1: 96 peptides, 21 chains. Longest chain 8 peptides. Score 0.257 Round 2: 98 peptides, 19 chains. Longest chain 8 peptides. Score 0.331 Round 3: 87 peptides, 17 chains. Longest chain 10 peptides. Score 0.313 Round 4: 83 peptides, 16 chains. Longest chain 10 peptides. Score 0.314 Round 5: 93 peptides, 16 chains. Longest chain 10 peptides. Score 0.384 Taking the results from Round 5 Chains 16, Residues 77, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 4672 reflections ( 99.85 % complete ) and 4846 restraints for refining 2013 atoms. 4554 conditional restraints added. Observations/parameters ratio is 0.58 ------------------------------------------------------ Cycle 41: After refmac, R = 0.3381 (Rfree = 0.000) for 2013 atoms. Found 18 (18 requested) and removed 19 (9 requested) atoms. Cycle 42: After refmac, R = 0.2675 (Rfree = 0.000) for 2004 atoms. Found 18 (18 requested) and removed 14 (9 requested) atoms. Cycle 43: After refmac, R = 0.2179 (Rfree = 0.000) for 2003 atoms. Found 8 (18 requested) and removed 12 (9 requested) atoms. Cycle 44: After refmac, R = 0.2611 (Rfree = 0.000) for 1998 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 45: After refmac, R = 0.2522 (Rfree = 0.000) for 1998 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.21 3.73 Search for helices and strands: 0 residues in 0 chains, 2064 seeds are put forward NCS extension: 0 residues added, 2064 seeds are put forward Round 1: 69 peptides, 15 chains. Longest chain 7 peptides. Score 0.241 Round 2: 87 peptides, 18 chains. Longest chain 8 peptides. Score 0.282 Round 3: 83 peptides, 16 chains. Longest chain 8 peptides. Score 0.314 Round 4: 70 peptides, 14 chains. Longest chain 8 peptides. Score 0.281 Round 5: 75 peptides, 14 chains. Longest chain 9 peptides. Score 0.319 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 61, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ouw-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 4672 reflections ( 99.85 % complete ) and 4464 restraints for refining 1923 atoms. 4234 conditional restraints added. Observations/parameters ratio is 0.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3047 (Rfree = 0.000) for 1923 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2412 (Rfree = 0.000) for 1910 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2523 (Rfree = 0.000) for 1902 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2795 (Rfree = 0.000) for 1893 atoms. Found 0 (16 requested) and removed 8 (8 requested) atoms. Writing output files ... TimeTaking 32.55