null Mon 24 Dec 07:52:49 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2o08-3.6-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2o08-3.6-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2o08-3.6-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-parrot-noncs 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/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-parrot-noncs ############### 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 ============================================================ Mon 24 Dec 07:52:53 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/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2o08-3.6-parrot-noncs/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-noncs.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-noncs.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 3345 atoms. Observations/parameters ratio is 0.48 ------------------------------------------------------ Starting model: R = 0.3348 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2662 (Rfree = 0.000) for 3345 atoms. Found 18 (21 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.45 2.89 Search for helices and strands: 0 residues in 0 chains, 3446 seeds are put forward NCS extension: 0 residues added, 3446 seeds are put forward Round 1: 188 peptides, 33 chains. Longest chain 12 peptides. Score 0.361 Round 2: 224 peptides, 30 chains. Longest chain 21 peptides. Score 0.503 Round 3: 226 peptides, 27 chains. Longest chain 18 peptides. Score 0.543 Round 4: 230 peptides, 27 chains. Longest chain 19 peptides. Score 0.553 Round 5: 226 peptides, 26 chains. Longest chain 24 peptides. Score 0.555 Taking the results from Round 5 Chains 26, Residues 200, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 6083 restraints for refining 2727 atoms. 5309 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2767 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 2: After refmac, R = 0.2670 (Rfree = 0.000) for 2676 atoms. Found 13 (17 requested) and removed 12 (8 requested) atoms. Cycle 3: After refmac, R = 0.2499 (Rfree = 0.000) for 2658 atoms. Found 17 (17 requested) and removed 9 (8 requested) atoms. Cycle 4: After refmac, R = 0.2518 (Rfree = 0.000) for 2652 atoms. Found 17 (17 requested) and removed 10 (8 requested) atoms. Cycle 5: After refmac, R = 0.2489 (Rfree = 0.000) for 2638 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.49 2.92 Search for helices and strands: 0 residues in 0 chains, 2797 seeds are put forward NCS extension: 29 residues added (3 deleted due to clashes), 2826 seeds are put forward Round 1: 215 peptides, 36 chains. Longest chain 17 peptides. Score 0.404 Round 2: 226 peptides, 29 chains. Longest chain 23 peptides. Score 0.520 Round 3: 227 peptides, 31 chains. Longest chain 16 peptides. Score 0.499 Round 4: 237 peptides, 28 chains. Longest chain 26 peptides. Score 0.559 Round 5: 234 peptides, 31 chains. Longest chain 21 peptides. Score 0.517 Taking the results from Round 4 Chains 28, Residues 209, Estimated correctness of the model 0.0 % 1 chains (25 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5682 restraints for refining 2727 atoms. 4752 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2833 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 15 (8 requested) atoms. Cycle 7: After refmac, R = 0.2700 (Rfree = 0.000) for 2690 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 8: After refmac, R = 0.2728 (Rfree = 0.000) for 2677 atoms. Found 15 (17 requested) and removed 15 (8 requested) atoms. Cycle 9: After refmac, R = 0.2618 (Rfree = 0.000) for 2648 atoms. Found 17 (17 requested) and removed 11 (8 requested) atoms. Cycle 10: After refmac, R = 0.2602 (Rfree = 0.000) for 2636 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.44 2.88 Search for helices and strands: 0 residues in 0 chains, 2750 seeds are put forward NCS extension: 32 residues added (2 deleted due to clashes), 2782 seeds are put forward Round 1: 197 peptides, 35 chains. Longest chain 10 peptides. Score 0.362 Round 2: 215 peptides, 29 chains. Longest chain 20 peptides. Score 0.491 Round 3: 213 peptides, 26 chains. Longest chain 25 peptides. Score 0.522 Round 4: 233 peptides, 27 chains. Longest chain 34 peptides. Score 0.561 Round 5: 213 peptides, 28 chains. Longest chain 15 peptides. Score 0.498 Taking the results from Round 4 Chains 28, Residues 206, Estimated correctness of the model 0.0 % 1 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5599 restraints for refining 2726 atoms. 4657 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2822 (Rfree = 0.000) for 2726 atoms. Found 17 (17 requested) and removed 31 (8 requested) atoms. Cycle 12: After refmac, R = 0.2552 (Rfree = 0.000) for 2692 atoms. Found 17 (17 requested) and removed 25 (8 requested) atoms. Cycle 13: After refmac, R = 0.2532 (Rfree = 0.000) for 2676 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 14: After refmac, R = 0.2505 (Rfree = 0.000) for 2667 atoms. Found 17 (17 requested) and removed 27 (8 requested) atoms. Cycle 15: After refmac, R = 0.2427 (Rfree = 0.000) for 2648 atoms. Found 14 (17 requested) and removed 18 (8 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.79 3.17 Search for helices and strands: 0 residues in 0 chains, 2782 seeds are put forward NCS extension: 38 residues added (2 deleted due to clashes), 2820 seeds are put forward Round 1: 215 peptides, 34 chains. Longest chain 17 peptides. Score 0.429 Round 2: 216 peptides, 28 chains. Longest chain 21 peptides. Score 0.506 Round 3: 227 peptides, 30 chains. Longest chain 15 peptides. Score 0.511 Round 4: 233 peptides, 28 chains. Longest chain 19 peptides. Score 0.549 Round 5: 225 peptides, 27 chains. Longest chain 20 peptides. Score 0.541 Taking the results from Round 4 Chains 28, Residues 205, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5972 restraints for refining 2727 atoms. 5180 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2548 (Rfree = 0.000) for 2727 atoms. Found 15 (17 requested) and removed 15 (8 requested) atoms. Cycle 17: After refmac, R = 0.2550 (Rfree = 0.000) for 2712 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 18: After refmac, R = 0.2549 (Rfree = 0.000) for 2698 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 19: After refmac, R = 0.2445 (Rfree = 0.000) for 2690 atoms. Found 17 (17 requested) and removed 13 (8 requested) atoms. Cycle 20: After refmac, R = 0.2230 (Rfree = 0.000) for 2688 atoms. Found 6 (17 requested) and removed 8 (8 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.52 2.95 Search for helices and strands: 0 residues in 0 chains, 2847 seeds are put forward NCS extension: 20 residues added (1 deleted due to clashes), 2867 seeds are put forward Round 1: 200 peptides, 31 chains. Longest chain 17 peptides. Score 0.424 Round 2: 200 peptides, 29 chains. Longest chain 13 peptides. Score 0.450 Round 3: 205 peptides, 31 chains. Longest chain 18 peptides. Score 0.439 Round 4: 212 peptides, 27 chains. Longest chain 20 peptides. Score 0.508 Round 5: 202 peptides, 28 chains. Longest chain 22 peptides. Score 0.468 Taking the results from Round 4 Chains 27, Residues 185, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5988 restraints for refining 2727 atoms. 5260 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2519 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 22: After refmac, R = 0.2442 (Rfree = 0.000) for 2714 atoms. Found 11 (17 requested) and removed 11 (8 requested) atoms. Cycle 23: After refmac, R = 0.2393 (Rfree = 0.000) for 2696 atoms. Found 9 (17 requested) and removed 11 (8 requested) atoms. Cycle 24: After refmac, R = 0.2257 (Rfree = 0.000) for 2685 atoms. Found 5 (17 requested) and removed 12 (8 requested) atoms. Cycle 25: After refmac, R = 0.2303 (Rfree = 0.000) for 2672 atoms. Found 9 (17 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.46 2.90 Search for helices and strands: 0 residues in 0 chains, 2822 seeds are put forward NCS extension: 19 residues added (2 deleted due to clashes), 2841 seeds are put forward Round 1: 179 peptides, 32 chains. Longest chain 13 peptides. Score 0.346 Round 2: 196 peptides, 29 chains. Longest chain 19 peptides. Score 0.438 Round 3: 212 peptides, 29 chains. Longest chain 20 peptides. Score 0.483 Round 4: 218 peptides, 30 chains. Longest chain 19 peptides. Score 0.487 Round 5: 214 peptides, 29 chains. Longest chain 19 peptides. Score 0.489 Taking the results from Round 5 Chains 30, Residues 185, Estimated correctness of the model 0.0 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5999 restraints for refining 2726 atoms. 5261 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2698 (Rfree = 0.000) for 2726 atoms. Found 17 (17 requested) and removed 22 (8 requested) atoms. Cycle 27: After refmac, R = 0.2680 (Rfree = 0.000) for 2706 atoms. Found 17 (17 requested) and removed 19 (8 requested) atoms. Cycle 28: After refmac, R = 0.2565 (Rfree = 0.000) for 2695 atoms. Found 17 (17 requested) and removed 17 (8 requested) atoms. Cycle 29: After refmac, R = 0.2471 (Rfree = 0.000) for 2688 atoms. Found 17 (17 requested) and removed 12 (8 requested) atoms. Cycle 30: After refmac, R = 0.2440 (Rfree = 0.000) for 2687 atoms. Found 17 (17 requested) and removed 21 (8 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.49 2.92 Search for helices and strands: 0 residues in 0 chains, 2807 seeds are put forward NCS extension: 30 residues added (2 deleted due to clashes), 2837 seeds are put forward Round 1: 173 peptides, 31 chains. Longest chain 11 peptides. Score 0.341 Round 2: 195 peptides, 26 chains. Longest chain 18 peptides. Score 0.474 Round 3: 204 peptides, 30 chains. Longest chain 14 peptides. Score 0.448 Round 4: 218 peptides, 33 chains. Longest chain 14 peptides. Score 0.450 Round 5: 211 peptides, 28 chains. Longest chain 17 peptides. Score 0.493 Taking the results from Round 5 Chains 28, Residues 183, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5941 restraints for refining 2727 atoms. 5192 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2723 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 50 (8 requested) atoms. Cycle 32: After refmac, R = 0.2702 (Rfree = 0.000) for 2687 atoms. Found 13 (17 requested) and removed 25 (8 requested) atoms. Cycle 33: After refmac, R = 0.2599 (Rfree = 0.000) for 2670 atoms. Found 5 (17 requested) and removed 21 (8 requested) atoms. Cycle 34: After refmac, R = 0.2542 (Rfree = 0.000) for 2651 atoms. Found 4 (17 requested) and removed 24 (8 requested) atoms. Cycle 35: After refmac, R = 0.2445 (Rfree = 0.000) for 2628 atoms. Found 6 (16 requested) and removed 13 (8 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.49 2.92 Search for helices and strands: 0 residues in 0 chains, 2728 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 2744 seeds are put forward Round 1: 174 peptides, 35 chains. Longest chain 9 peptides. Score 0.288 Round 2: 200 peptides, 33 chains. Longest chain 14 peptides. Score 0.398 Round 3: 198 peptides, 30 chains. Longest chain 12 peptides. Score 0.431 Round 4: 212 peptides, 31 chains. Longest chain 14 peptides. Score 0.458 Round 5: 217 peptides, 32 chains. Longest chain 14 peptides. Score 0.460 Taking the results from Round 5 Chains 33, Residues 185, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 5901 restraints for refining 2727 atoms. 5128 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2850 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 20 (8 requested) atoms. Cycle 37: After refmac, R = 0.2677 (Rfree = 0.000) for 2711 atoms. Found 12 (17 requested) and removed 23 (8 requested) atoms. Cycle 38: After refmac, R = 0.2722 (Rfree = 0.000) for 2681 atoms. Found 17 (17 requested) and removed 16 (8 requested) atoms. Cycle 39: After refmac, R = 0.2510 (Rfree = 0.000) for 2667 atoms. Found 16 (17 requested) and removed 18 (8 requested) atoms. Cycle 40: After refmac, R = 0.2604 (Rfree = 0.000) for 2657 atoms. Found 17 (17 requested) and removed 14 (8 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.75 3.14 Search for helices and strands: 0 residues in 0 chains, 2787 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 2801 seeds are put forward Round 1: 153 peptides, 33 chains. Longest chain 8 peptides. Score 0.245 Round 2: 181 peptides, 33 chains. Longest chain 10 peptides. Score 0.339 Round 3: 194 peptides, 35 chains. Longest chain 10 peptides. Score 0.353 Round 4: 190 peptides, 32 chains. Longest chain 14 peptides. Score 0.381 Round 5: 202 peptides, 34 chains. Longest chain 11 peptides. Score 0.391 Taking the results from Round 5 Chains 34, Residues 168, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 6473 reflections ( 97.75 % complete ) and 6137 restraints for refining 2727 atoms. 5499 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2861 (Rfree = 0.000) for 2727 atoms. Found 17 (17 requested) and removed 47 (8 requested) atoms. Cycle 42: After refmac, R = 0.2687 (Rfree = 0.000) for 2677 atoms. Found 11 (17 requested) and removed 36 (8 requested) atoms. Cycle 43: After refmac, R = 0.2733 (Rfree = 0.000) for 2643 atoms. Found 17 (17 requested) and removed 28 (8 requested) atoms. Cycle 44: After refmac, R = 0.2603 (Rfree = 0.000) for 2628 atoms. Found 15 (16 requested) and removed 18 (8 requested) atoms. Cycle 45: After refmac, R = 0.2609 (Rfree = 0.000) for 2620 atoms. Found 16 (16 requested) and removed 28 (8 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.55 2.97 Search for helices and strands: 0 residues in 0 chains, 2729 seeds are put forward NCS extension: 0 residues added, 2729 seeds are put forward Round 1: 156 peptides, 35 chains. Longest chain 7 peptides. Score 0.226 Round 2: 168 peptides, 31 chains. Longest chain 12 peptides. Score 0.325 Round 3: 166 peptides, 31 chains. Longest chain 11 peptides. Score 0.318 Round 4: 167 peptides, 27 chains. Longest chain 13 peptides. Score 0.378 Round 5: 159 peptides, 26 chains. Longest chain 14 peptides. Score 0.367 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 27, Residues 140, Estimated correctness of the model 0.0 % 2 chains (9 residues) have been docked in sequence Sequence coverage is 6 % Consider running further cycles of model building using 2o08-3_warpNtrace.pdb as input Building loops using Loopy2018 27 chains (140 residues) following loop building 2 chains (9 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6473 reflections ( 97.75 % complete ) and 6098 restraints for refining 2726 atoms. 5539 conditional restraints added. Observations/parameters ratio is 0.59 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2673 (Rfree = 0.000) for 2726 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 47: After refmac, R = 0.2751 (Rfree = 0.000) for 2691 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 48: After refmac, R = 0.2606 (Rfree = 0.000) for 2660 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Cycle 49: After refmac, R = 0.2700 (Rfree = 0.000) for 2636 atoms. Found 0 (17 requested) and removed 8 (8 requested) atoms. Writing output files ... Normal termination of warpNtrace Mon 24 Dec 08:26:56 GMT 2018 Job finished. TimeTaking 34.11 Used memory is bytes: 6929336