Sun 23 Dec 22:22:49 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 2o08-3.6-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2o08-3.6-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2o08-3.6-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-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/2o08-3.6-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-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 ============================================================ Sun 23 Dec 22:22:59 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/2o08-3.6-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-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 369 and 0 Target number of residues in the AU: 369 Target solvent content: 0.6334 Checking the provided sequence file Detected sequence length: 188 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 376 Adjusted target solvent content: 0.63 Input MTZ file: 2o08-3.6-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: 20 Cell parameters: 87.690 166.470 74.630 90.000 90.000 90.000 Input sequence file: 2o08-3.6-parrot-hancs.fasta_lf Building free atoms model in initial map for 3008 target number of atoms Had to go as low as 0.90 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: 83.235 3.600 Wilson plot Bfac: 68.09 6473 reflections ( 97.75 % complete ) and 0 restraints for refining 3339 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3295 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2963 (Rfree = 0.000) for 3339 atoms. Found 21 (21 requested) and removed 16 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.50 2.93 Search for helices and strands: 0 residues in 0 chains, 3443 seeds are put forward NCS extension: 0 residues added, 3443 seeds are put forward Round 1: 197 peptides, 31 chains. Longest chain 18 peptides. Score 0.415 Round 2: 213 peptides, 28 chains. Longest chain 19 peptides. Score 0.498 Round 3: 230 peptides, 32 chains. Longest chain 24 peptides. Score 0.495 Round 4: 228 peptides, 30 chains. Longest chain 21 peptides. Score 0.514 Round 5: 234 peptides, 31 chains. Longest chain 22 peptides. Score 0.517 Taking the results from Round 5 Chains 33, Residues 203, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5974 restraints for refining 2725 atoms. 5163 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2665 (Rfree = 0.000) for 2725 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 2: After refmac, R = 0.2599 (Rfree = 0.000) for 2695 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. Cycle 3: After refmac, R = 0.2623 (Rfree = 0.000) for 2671 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 4: After refmac, R = 0.2479 (Rfree = 0.000) for 2651 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 5: After refmac, R = 0.2606 (Rfree = 0.000) for 2642 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 2.91 Search for helices and strands: 0 residues in 0 chains, 2813 seeds are put forward NCS extension: 18 residues added (1 deleted due to clashes), 2831 seeds are put forward Round 1: 219 peptides, 37 chains. Longest chain 13 peptides. Score 0.403 Round 2: 243 peptides, 33 chains. Longest chain 20 peptides. Score 0.517 Round 3: 235 peptides, 27 chains. Longest chain 21 peptides. Score 0.565 Round 4: 231 peptides, 30 chains. Longest chain 21 peptides. Score 0.521 Round 5: 238 peptides, 30 chains. Longest chain 21 peptides. Score 0.539 Taking the results from Round 3 Chains 28, Residues 208, Estimated correctness of the model 0.5 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5899 restraints for refining 2727 atoms. 5065 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2428 (Rfree = 0.000) for 2727 atoms. Found 16 (17 requested) and removed 17 (8 requested) atoms. Cycle 7: After refmac, R = 0.2405 (Rfree = 0.000) for 2711 atoms. Found 16 (17 requested) and removed 13 (8 requested) atoms. Cycle 8: After refmac, R = 0.2302 (Rfree = 0.000) for 2700 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 9: After refmac, R = 0.2298 (Rfree = 0.000) for 2697 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. Cycle 10: After refmac, R = 0.2044 (Rfree = 0.000) for 2691 atoms. Found 5 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.42 2.86 Search for helices and strands: 0 residues in 0 chains, 2868 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 2894 seeds are put forward Round 1: 232 peptides, 35 chains. Longest chain 14 peptides. Score 0.465 Round 2: 234 peptides, 30 chains. Longest chain 19 peptides. Score 0.529 Round 3: 230 peptides, 28 chains. Longest chain 20 peptides. Score 0.542 Round 4: 228 peptides, 31 chains. Longest chain 15 peptides. Score 0.502 Round 5: 230 peptides, 29 chains. Longest chain 18 peptides. Score 0.530 Taking the results from Round 3 Chains 28, Residues 202, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 6017 restraints for refining 2724 atoms. 5237 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2631 (Rfree = 0.000) for 2724 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 12: After refmac, R = 0.2491 (Rfree = 0.000) for 2701 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 13: After refmac, R = 0.2550 (Rfree = 0.000) for 2687 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 14: After refmac, R = 0.2493 (Rfree = 0.000) for 2684 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 15: After refmac, R = 0.2555 (Rfree = 0.000) for 2678 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.44 2.88 Search for helices and strands: 0 residues in 0 chains, 2854 seeds are put forward NCS extension: 13 residues added (3 deleted due to clashes), 2867 seeds are put forward Round 1: 198 peptides, 33 chains. Longest chain 12 peptides. Score 0.392 Round 2: 225 peptides, 34 chains. Longest chain 15 peptides. Score 0.457 Round 3: 231 peptides, 33 chains. Longest chain 13 peptides. Score 0.486 Round 4: 221 peptides, 31 chains. Longest chain 17 peptides. Score 0.483 Round 5: 233 peptides, 32 chains. Longest chain 18 peptides. Score 0.503 Taking the results from Round 5 Chains 33, Residues 201, Estimated correctness of the model 0.0 % 1 chains (11 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5821 restraints for refining 2726 atoms. 5001 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2882 (Rfree = 0.000) for 2726 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 17: After refmac, R = 0.2766 (Rfree = 0.000) for 2712 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 18: After refmac, R = 0.2662 (Rfree = 0.000) for 2695 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 19: After refmac, R = 0.2600 (Rfree = 0.000) for 2684 atoms. Found 16 (17 requested) and removed 12 (8 requested) atoms. Cycle 20: After refmac, R = 0.2371 (Rfree = 0.000) for 2680 atoms. Found 6 (17 requested) and removed 9 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.47 2.91 Search for helices and strands: 0 residues in 0 chains, 2826 seeds are put forward NCS extension: 20 residues added (2 deleted due to clashes), 2846 seeds are put forward Round 1: 190 peptides, 31 chains. Longest chain 16 peptides. Score 0.394 Round 2: 226 peptides, 30 chains. Longest chain 18 peptides. Score 0.508 Round 3: 202 peptides, 30 chains. Longest chain 12 peptides. Score 0.443 Round 4: 229 peptides, 30 chains. Longest chain 25 peptides. Score 0.516 Round 5: 222 peptides, 28 chains. Longest chain 18 peptides. Score 0.522 Taking the results from Round 5 Chains 29, Residues 194, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5940 restraints for refining 2725 atoms. 5161 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2743 (Rfree = 0.000) for 2725 atoms. Found 14 (17 requested) and removed 9 (8 requested) atoms. Cycle 22: After refmac, R = 0.2655 (Rfree = 0.000) for 2713 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.2666 (Rfree = 0.000) for 2716 atoms. Found 10 (17 requested) and removed 13 (8 requested) atoms. Cycle 24: After refmac, R = 0.2540 (Rfree = 0.000) for 2706 atoms. Found 4 (17 requested) and removed 9 (8 requested) atoms. Cycle 25: After refmac, R = 0.2545 (Rfree = 0.000) for 2698 atoms. Found 4 (17 requested) and removed 10 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.43 2.87 Search for helices and strands: 0 residues in 0 chains, 2865 seeds are put forward NCS extension: 23 residues added (2 deleted due to clashes), 2888 seeds are put forward Round 1: 199 peptides, 36 chains. Longest chain 13 peptides. Score 0.355 Round 2: 203 peptides, 27 chains. Longest chain 19 peptides. Score 0.483 Round 3: 208 peptides, 29 chains. Longest chain 25 peptides. Score 0.472 Round 4: 213 peptides, 26 chains. Longest chain 15 peptides. Score 0.522 Round 5: 226 peptides, 32 chains. Longest chain 19 peptides. Score 0.485 Taking the results from Round 4 Chains 26, Residues 187, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 6046 restraints for refining 2727 atoms. 5324 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2757 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 27: After refmac, R = 0.2620 (Rfree = 0.000) for 2722 atoms. Found 10 (17 requested) and removed 11 (8 requested) atoms. Cycle 28: After refmac, R = 0.2502 (Rfree = 0.000) for 2714 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 29: After refmac, R = 0.2511 (Rfree = 0.000) for 2709 atoms. Found 8 (17 requested) and removed 10 (8 requested) atoms. Cycle 30: After refmac, R = 0.2510 (Rfree = 0.000) for 2706 atoms. Found 2 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.45 2.89 Search for helices and strands: 0 residues in 0 chains, 2822 seeds are put forward NCS extension: 0 residues added, 2822 seeds are put forward Round 1: 185 peptides, 31 chains. Longest chain 22 peptides. Score 0.379 Round 2: 211 peptides, 26 chains. Longest chain 26 peptides. Score 0.517 Round 3: 210 peptides, 30 chains. Longest chain 19 peptides. Score 0.465 Round 4: 209 peptides, 29 chains. Longest chain 18 peptides. Score 0.475 Round 5: 219 peptides, 29 chains. Longest chain 22 peptides. Score 0.502 Taking the results from Round 2 Chains 28, Residues 185, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5897 restraints for refining 2726 atoms. 5140 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2699 (Rfree = 0.000) for 2726 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 32: After refmac, R = 0.2650 (Rfree = 0.000) for 2719 atoms. Found 11 (17 requested) and removed 14 (8 requested) atoms. Cycle 33: After refmac, R = 0.2538 (Rfree = 0.000) for 2712 atoms. Found 9 (17 requested) and removed 10 (8 requested) atoms. Cycle 34: After refmac, R = 0.2524 (Rfree = 0.000) for 2704 atoms. Found 5 (17 requested) and removed 10 (8 requested) atoms. Cycle 35: After refmac, R = 0.2486 (Rfree = 0.000) for 2695 atoms. Found 3 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.44 2.88 Search for helices and strands: 0 residues in 0 chains, 2792 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 2814 seeds are put forward Round 1: 168 peptides, 28 chains. Longest chain 12 peptides. Score 0.367 Round 2: 192 peptides, 25 chains. Longest chain 16 peptides. Score 0.478 Round 3: 182 peptides, 26 chains. Longest chain 14 peptides. Score 0.437 Round 4: 182 peptides, 25 chains. Longest chain 20 peptides. Score 0.450 Round 5: 183 peptides, 22 chains. Longest chain 19 peptides. Score 0.492 Taking the results from Round 5 Chains 22, Residues 161, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 6302 restraints for refining 2727 atoms. 5680 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2571 (Rfree = 0.000) for 2727 atoms. Found 15 (17 requested) and removed 11 (8 requested) atoms. Cycle 37: After refmac, R = 0.2727 (Rfree = 0.000) for 2712 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 38: After refmac, R = 0.2784 (Rfree = 0.000) for 2702 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. Cycle 39: After refmac, R = 0.2700 (Rfree = 0.000) for 2678 atoms. Found 17 (17 requested) and removed 18 (8 requested) atoms. Cycle 40: After refmac, R = 0.2771 (Rfree = 0.000) for 2661 atoms. Found 17 (17 requested) and removed 23 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.52 2.95 Search for helices and strands: 0 residues in 0 chains, 2771 seeds are put forward NCS extension: 25 residues added (2 deleted due to clashes), 2796 seeds are put forward Round 1: 147 peptides, 30 chains. Longest chain 12 peptides. Score 0.268 Round 2: 174 peptides, 28 chains. Longest chain 13 peptides. Score 0.386 Round 3: 181 peptides, 28 chains. Longest chain 14 peptides. Score 0.407 Round 4: 166 peptides, 25 chains. Longest chain 14 peptides. Score 0.403 Round 5: 158 peptides, 24 chains. Longest chain 18 peptides. Score 0.392 Taking the results from Round 3 Chains 28, Residues 153, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 6158 restraints for refining 2711 atoms. 5574 conditional restraints added. Observations/parameters ratio is 0.60 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2966 (Rfree = 0.000) for 2711 atoms. Found 17 (17 requested) and removed 32 (8 requested) atoms. Cycle 42: After refmac, R = 0.2880 (Rfree = 0.000) for 2675 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 43: After refmac, R = 0.2907 (Rfree = 0.000) for 2663 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 44: After refmac, R = 0.2838 (Rfree = 0.000) for 2644 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 45: After refmac, R = 0.2732 (Rfree = 0.000) for 2635 atoms. Found 16 (16 requested) and removed 12 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 4.07 3.41 Search for helices and strands: 0 residues in 0 chains, 2771 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2791 seeds are put forward Round 1: 133 peptides, 28 chains. Longest chain 10 peptides. Score 0.248 Round 2: 175 peptides, 30 chains. Longest chain 11 peptides. Score 0.361 Round 3: 182 peptides, 29 chains. Longest chain 25 peptides. Score 0.397 Round 4: 178 peptides, 27 chains. Longest chain 19 peptides. Score 0.412 Round 5: 167 peptides, 26 chains. Longest chain 21 peptides. Score 0.392 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 151, 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 2o08-3_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6473 reflections ( 97.75 % complete ) and 6087 restraints for refining 2727 atoms. 5510 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2842 (Rfree = 0.000) for 2727 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2749 (Rfree = 0.000) for 2707 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2720 (Rfree = 0.000) for 2694 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2640 (Rfree = 0.000) for 2673 atoms. TimeTaking 51.7