null Tue 25 Dec 19:27:57 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2oyo-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oyo-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-4.0-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:06 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/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oyo-4.0-parrot-hancs/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 254 and 0 Target number of residues in the AU: 254 Target solvent content: 0.6714 Checking the provided sequence file Detected sequence length: 196 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 392 Adjusted target solvent content: 0.49 Input MTZ file: 2oyo-4.0-parrot-hancs.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: 155 Cell parameters: 135.664 135.664 118.109 90.000 90.000 120.000 Input sequence file: 2oyo-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 3136 target number of atoms Had to go as low as 0.85 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: 83.295 4.001 Wilson plot Bfac: 93.40 *** WARNING *** *** WARNING *** This resolution is too low for ARP/wARP protein chain tracing *** WARNING *** 3640 reflections ( 99.75 % complete ) and 0 restraints for refining 3466 atoms. Observations/parameters ratio is 0.26 ------------------------------------------------------ Starting model: R = 0.3365 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3078 (Rfree = 0.000) for 3466 atoms. Found 16 (16 requested) and removed 40 (8 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.82 3.87 Search for helices and strands: 0 residues in 0 chains, 3528 seeds are put forward NCS extension: 0 residues added, 3528 seeds are put forward Round 1: 120 peptides, 24 chains. Longest chain 9 peptides. Score 0.282 Round 2: 147 peptides, 23 chains. Longest chain 11 peptides. Score 0.413 Round 3: 147 peptides, 21 chains. Longest chain 9 peptides. Score 0.447 Round 4: 151 peptides, 22 chains. Longest chain 10 peptides. Score 0.445 Round 5: 148 peptides, 22 chains. Longest chain 13 peptides. Score 0.434 Taking the results from Round 3 Chains 21, Residues 126, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6957 restraints for refining 2829 atoms. 6456 conditional restraints added. Observations/parameters ratio is 0.32 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2488 (Rfree = 0.000) for 2829 atoms. Found 10 (13 requested) and removed 21 (6 requested) atoms. Cycle 2: After refmac, R = 0.2224 (Rfree = 0.000) for 2789 atoms. Found 11 (13 requested) and removed 13 (6 requested) atoms. Cycle 3: After refmac, R = 0.1702 (Rfree = 0.000) for 2766 atoms. Found 0 (13 requested) and removed 13 (6 requested) atoms. Cycle 4: After refmac, R = 0.1840 (Rfree = 0.000) for 2735 atoms. Found 8 (13 requested) and removed 8 (6 requested) atoms. Cycle 5: After refmac, R = 0.2119 (Rfree = 0.000) for 2729 atoms. Found 11 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.78 3.83 Search for helices and strands: 0 residues in 0 chains, 2857 seeds are put forward NCS extension: 0 residues added, 2857 seeds are put forward Round 1: 138 peptides, 28 chains. Longest chain 9 peptides. Score 0.287 Round 2: 156 peptides, 28 chains. Longest chain 13 peptides. Score 0.362 Round 3: 156 peptides, 24 chains. Longest chain 11 peptides. Score 0.430 Round 4: 168 peptides, 25 chains. Longest chain 17 peptides. Score 0.458 Round 5: 162 peptides, 25 chains. Longest chain 13 peptides. Score 0.436 Taking the results from Round 4 Chains 25, Residues 143, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6333 restraints for refining 2720 atoms. 5732 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2132 (Rfree = 0.000) for 2720 atoms. Found 11 (12 requested) and removed 29 (6 requested) atoms. Cycle 7: After refmac, R = 0.2035 (Rfree = 0.000) for 2662 atoms. Found 3 (12 requested) and removed 17 (6 requested) atoms. Cycle 8: After refmac, R = 0.2075 (Rfree = 0.000) for 2617 atoms. Found 9 (12 requested) and removed 16 (6 requested) atoms. Cycle 9: After refmac, R = 0.1891 (Rfree = 0.000) for 2588 atoms. Found 3 (12 requested) and removed 18 (6 requested) atoms. Cycle 10: After refmac, R = 0.1873 (Rfree = 0.000) for 2558 atoms. Found 6 (12 requested) and removed 13 (6 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.80 3.85 Search for helices and strands: 0 residues in 0 chains, 2657 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2683 seeds are put forward Round 1: 132 peptides, 25 chains. Longest chain 11 peptides. Score 0.316 Round 2: 149 peptides, 24 chains. Longest chain 13 peptides. Score 0.403 Round 3: 155 peptides, 25 chains. Longest chain 13 peptides. Score 0.409 Round 4: 157 peptides, 24 chains. Longest chain 16 peptides. Score 0.434 Round 5: 166 peptides, 22 chains. Longest chain 17 peptides. Score 0.499 Taking the results from Round 5 Chains 23, Residues 144, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 5923 restraints for refining 2601 atoms. 5332 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2089 (Rfree = 0.000) for 2601 atoms. Found 10 (12 requested) and removed 34 (6 requested) atoms. Cycle 12: After refmac, R = 0.1961 (Rfree = 0.000) for 2555 atoms. Found 7 (12 requested) and removed 18 (6 requested) atoms. Cycle 13: After refmac, R = 0.1909 (Rfree = 0.000) for 2533 atoms. Found 11 (12 requested) and removed 19 (6 requested) atoms. Cycle 14: After refmac, R = 0.1880 (Rfree = 0.000) for 2516 atoms. Found 11 (11 requested) and removed 17 (5 requested) atoms. Cycle 15: After refmac, R = 0.1970 (Rfree = 0.000) for 2506 atoms. Found 11 (11 requested) and removed 11 (5 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 2639 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2659 seeds are put forward Round 1: 136 peptides, 27 chains. Longest chain 9 peptides. Score 0.296 Round 2: 143 peptides, 23 chains. Longest chain 12 peptides. Score 0.397 Round 3: 148 peptides, 22 chains. Longest chain 14 peptides. Score 0.434 Round 4: 149 peptides, 20 chains. Longest chain 14 peptides. Score 0.471 Round 5: 160 peptides, 22 chains. Longest chain 15 peptides. Score 0.478 Taking the results from Round 5 Chains 22, Residues 138, Estimated correctness of the model 0.0 % 1 chains (7 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6118 restraints for refining 2695 atoms. 5555 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1945 (Rfree = 0.000) for 2695 atoms. Found 12 (12 requested) and removed 26 (6 requested) atoms. Cycle 17: After refmac, R = 0.2038 (Rfree = 0.000) for 2656 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 18: After refmac, R = 0.1509 (Rfree = 0.000) for 2629 atoms. Found 6 (12 requested) and removed 8 (6 requested) atoms. Cycle 19: After refmac, R = 0.1420 (Rfree = 0.000) for 2622 atoms. Found 0 (12 requested) and removed 7 (6 requested) atoms. Cycle 20: After refmac, R = 0.1427 (Rfree = 0.000) for 2611 atoms. Found 3 (12 requested) and removed 8 (6 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.81 3.86 Search for helices and strands: 0 residues in 0 chains, 2711 seeds are put forward NCS extension: 14 residues added (1 deleted due to clashes), 2725 seeds are put forward Round 1: 142 peptides, 29 chains. Longest chain 11 peptides. Score 0.286 Round 2: 162 peptides, 28 chains. Longest chain 10 peptides. Score 0.386 Round 3: 166 peptides, 27 chains. Longest chain 13 peptides. Score 0.418 Round 4: 156 peptides, 22 chains. Longest chain 14 peptides. Score 0.463 Round 5: 159 peptides, 24 chains. Longest chain 13 peptides. Score 0.441 Taking the results from Round 4 Chains 22, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6426 restraints for refining 2718 atoms. 5912 conditional restraints added. Observations/parameters ratio is 0.33 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1902 (Rfree = 0.000) for 2718 atoms. Found 12 (12 requested) and removed 20 (6 requested) atoms. Cycle 22: After refmac, R = 0.2005 (Rfree = 0.000) for 2699 atoms. Found 12 (12 requested) and removed 21 (6 requested) atoms. Cycle 23: After refmac, R = 0.1971 (Rfree = 0.000) for 2677 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 24: After refmac, R = 0.2133 (Rfree = 0.000) for 2661 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 25: After refmac, R = 0.1939 (Rfree = 0.000) for 2650 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.79 3.84 Search for helices and strands: 0 residues in 0 chains, 2792 seeds are put forward NCS extension: 0 residues added, 2792 seeds are put forward Round 1: 133 peptides, 28 chains. Longest chain 8 peptides. Score 0.265 Round 2: 141 peptides, 26 chains. Longest chain 10 peptides. Score 0.336 Round 3: 152 peptides, 26 chains. Longest chain 13 peptides. Score 0.381 Round 4: 151 peptides, 24 chains. Longest chain 16 peptides. Score 0.411 Round 5: 146 peptides, 23 chains. Longest chain 14 peptides. Score 0.409 Taking the results from Round 4 Chains 24, Residues 127, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6424 restraints for refining 2711 atoms. 5940 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1964 (Rfree = 0.000) for 2711 atoms. Found 12 (12 requested) and removed 22 (6 requested) atoms. Cycle 27: After refmac, R = 0.1922 (Rfree = 0.000) for 2678 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 28: After refmac, R = 0.1890 (Rfree = 0.000) for 2667 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 29: After refmac, R = 0.2095 (Rfree = 0.000) for 2657 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 30: After refmac, R = 0.1801 (Rfree = 0.000) for 2649 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.74 3.79 Search for helices and strands: 0 residues in 0 chains, 2809 seeds are put forward NCS extension: 0 residues added, 2809 seeds are put forward Round 1: 106 peptides, 22 chains. Longest chain 8 peptides. Score 0.257 Round 2: 135 peptides, 25 chains. Longest chain 9 peptides. Score 0.329 Round 3: 137 peptides, 22 chains. Longest chain 15 peptides. Score 0.391 Round 4: 137 peptides, 25 chains. Longest chain 10 peptides. Score 0.337 Round 5: 143 peptides, 24 chains. Longest chain 12 peptides. Score 0.379 Taking the results from Round 3 Chains 22, Residues 115, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6359 restraints for refining 2672 atoms. 5921 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2162 (Rfree = 0.000) for 2672 atoms. Found 12 (12 requested) and removed 29 (6 requested) atoms. Cycle 32: After refmac, R = 0.2123 (Rfree = 0.000) for 2637 atoms. Found 12 (12 requested) and removed 14 (6 requested) atoms. Cycle 33: After refmac, R = 0.2065 (Rfree = 0.000) for 2623 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 34: After refmac, R = 0.1974 (Rfree = 0.000) for 2616 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 35: After refmac, R = 0.2160 (Rfree = 0.000) for 2603 atoms. Found 12 (12 requested) and removed 16 (6 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.71 3.76 Search for helices and strands: 0 residues in 0 chains, 2732 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 2747 seeds are put forward Round 1: 103 peptides, 23 chains. Longest chain 7 peptides. Score 0.222 Round 2: 109 peptides, 19 chains. Longest chain 15 peptides. Score 0.329 Round 3: 109 peptides, 18 chains. Longest chain 16 peptides. Score 0.349 Round 4: 112 peptides, 17 chains. Longest chain 17 peptides. Score 0.380 Round 5: 124 peptides, 22 chains. Longest chain 17 peptides. Score 0.337 Taking the results from Round 4 Chains 17, Residues 95, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 6249 restraints for refining 2617 atoms. 5863 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2030 (Rfree = 0.000) for 2617 atoms. Found 12 (12 requested) and removed 11 (6 requested) atoms. Cycle 37: After refmac, R = 0.2111 (Rfree = 0.000) for 2602 atoms. Found 12 (12 requested) and removed 15 (6 requested) atoms. Cycle 38: After refmac, R = 0.2005 (Rfree = 0.000) for 2585 atoms. Found 12 (12 requested) and removed 13 (6 requested) atoms. Cycle 39: After refmac, R = 0.2114 (Rfree = 0.000) for 2576 atoms. Found 12 (12 requested) and removed 10 (6 requested) atoms. Cycle 40: After refmac, R = 0.1949 (Rfree = 0.000) for 2569 atoms. Found 12 (12 requested) and removed 9 (6 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.67 3.72 Search for helices and strands: 0 residues in 0 chains, 2697 seeds are put forward NCS extension: 0 residues added, 2697 seeds are put forward Round 1: 82 peptides, 19 chains. Longest chain 6 peptides. Score 0.199 Round 2: 113 peptides, 23 chains. Longest chain 8 peptides. Score 0.269 Round 3: 119 peptides, 24 chains. Longest chain 8 peptides. Score 0.277 Round 4: 126 peptides, 24 chains. Longest chain 8 peptides. Score 0.308 Round 5: 104 peptides, 21 chains. Longest chain 11 peptides. Score 0.267 Taking the results from Round 4 Chains 24, Residues 102, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3640 reflections ( 99.75 % complete ) and 5999 restraints for refining 2540 atoms. 5615 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1929 (Rfree = 0.000) for 2540 atoms. Found 12 (12 requested) and removed 19 (6 requested) atoms. Cycle 42: After refmac, R = 0.1894 (Rfree = 0.000) for 2515 atoms. Found 12 (12 requested) and removed 7 (6 requested) atoms. Cycle 43: After refmac, R = 0.1961 (Rfree = 0.000) for 2511 atoms. Found 11 (11 requested) and removed 13 (5 requested) atoms. Cycle 44: After refmac, R = 0.1870 (Rfree = 0.000) for 2502 atoms. Found 11 (11 requested) and removed 8 (5 requested) atoms. Cycle 45: After refmac, R = 0.1857 (Rfree = 0.000) for 2500 atoms. Found 11 (11 requested) and removed 10 (5 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.62 3.67 Search for helices and strands: 0 residues in 0 chains, 2633 seeds are put forward NCS extension: 0 residues added, 2633 seeds are put forward Round 1: 93 peptides, 21 chains. Longest chain 6 peptides. Score 0.214 Round 2: 115 peptides, 23 chains. Longest chain 10 peptides. Score 0.278 Round 3: 110 peptides, 22 chains. Longest chain 9 peptides. Score 0.275 Round 4: 108 peptides, 22 chains. Longest chain 9 peptides. Score 0.266 Round 5: 108 peptides, 21 chains. Longest chain 9 peptides. Score 0.286 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 21, Residues 87, 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 2oyo-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3640 reflections ( 99.75 % complete ) and 6197 restraints for refining 2573 atoms. 5870 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1965 (Rfree = 0.000) for 2573 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 47: After refmac, R = 0.2001 (Rfree = 0.000) for 2558 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 48: After refmac, R = 0.1942 (Rfree = 0.000) for 2543 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Cycle 49: After refmac, R = 0.1811 (Rfree = 0.000) for 2529 atoms. Found 0 (12 requested) and removed 6 (6 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:20:48 GMT 2018 Job finished. TimeTaking 52.86 Used memory is bytes: 16640840