Mon 24 Dec 07:27:54 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 2fqp-3.4-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-3.4-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2fqp-3.4-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-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/2fqp-3.4-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-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 07:27:58 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/2fqp-3.4-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2fqp-3.4-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 244 and 0 Target number of residues in the AU: 244 Target solvent content: 0.6100 Checking the provided sequence file Detected sequence length: 97 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 388 Adjusted target solvent content: 0.38 Input MTZ file: 2fqp-3.4-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: 4 Cell parameters: 35.909 92.640 53.056 90.000 106.409 90.000 Input sequence file: 2fqp-3.4-parrot-noncs.fasta_lf Building free atoms model in initial map for 3104 target number of atoms Had to go as low as 0.60 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: 50.895 3.400 Wilson plot Bfac: 56.75 3849 reflections ( 82.76 % complete ) and 0 restraints for refining 3423 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3272 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2837 (Rfree = 0.000) for 3423 atoms. Found 25 (25 requested) and removed 44 (12 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.12 3.67 Search for helices and strands: 0 residues in 0 chains, 3438 seeds are put forward NCS extension: 0 residues added, 3438 seeds are put forward Round 1: 98 peptides, 21 chains. Longest chain 7 peptides. Score 0.250 Round 2: 132 peptides, 25 chains. Longest chain 10 peptides. Score 0.341 Round 3: 146 peptides, 27 chains. Longest chain 12 peptides. Score 0.368 Round 4: 126 peptides, 22 chains. Longest chain 13 peptides. Score 0.375 Round 5: 137 peptides, 23 chains. Longest chain 13 peptides. Score 0.407 Taking the results from Round 5 Chains 23, Residues 114, Estimated correctness of the model 0.0 % 1 chains (12 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6600 restraints for refining 2820 atoms. 6111 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2071 (Rfree = 0.000) for 2820 atoms. Found 18 (21 requested) and removed 25 (10 requested) atoms. Cycle 2: After refmac, R = 0.1930 (Rfree = 0.000) for 2775 atoms. Found 9 (21 requested) and removed 11 (10 requested) atoms. Cycle 3: After refmac, R = 0.1891 (Rfree = 0.000) for 2758 atoms. Found 7 (20 requested) and removed 12 (10 requested) atoms. Cycle 4: After refmac, R = 0.1921 (Rfree = 0.000) for 2744 atoms. Found 4 (20 requested) and removed 12 (10 requested) atoms. Cycle 5: After refmac, R = 0.1953 (Rfree = 0.000) for 2729 atoms. Found 3 (20 requested) and removed 18 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.98 3.51 Search for helices and strands: 0 residues in 0 chains, 2765 seeds are put forward NCS extension: 24 residues added (0 deleted due to clashes), 2789 seeds are put forward Round 1: 119 peptides, 26 chains. Longest chain 10 peptides. Score 0.251 Round 2: 119 peptides, 24 chains. Longest chain 9 peptides. Score 0.296 Round 3: 119 peptides, 24 chains. Longest chain 8 peptides. Score 0.296 Round 4: 129 peptides, 27 chains. Longest chain 9 peptides. Score 0.282 Round 5: 147 peptides, 27 chains. Longest chain 10 peptides. Score 0.373 Taking the results from Round 5 Chains 27, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6316 restraints for refining 2667 atoms. 5863 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2039 (Rfree = 0.000) for 2667 atoms. Found 20 (20 requested) and removed 19 (10 requested) atoms. Cycle 7: After refmac, R = 0.1859 (Rfree = 0.000) for 2656 atoms. Found 9 (20 requested) and removed 14 (10 requested) atoms. Cycle 8: After refmac, R = 0.1774 (Rfree = 0.000) for 2647 atoms. Found 6 (20 requested) and removed 10 (10 requested) atoms. Cycle 9: After refmac, R = 0.1697 (Rfree = 0.000) for 2640 atoms. Found 2 (19 requested) and removed 10 (9 requested) atoms. Cycle 10: After refmac, R = 0.1655 (Rfree = 0.000) for 2629 atoms. Found 3 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.03 3.57 Search for helices and strands: 0 residues in 0 chains, 2676 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2679 seeds are put forward Round 1: 138 peptides, 29 chains. Longest chain 8 peptides. Score 0.286 Round 2: 147 peptides, 27 chains. Longest chain 15 peptides. Score 0.373 Round 3: 142 peptides, 26 chains. Longest chain 11 peptides. Score 0.369 Round 4: 151 peptides, 27 chains. Longest chain 10 peptides. Score 0.392 Round 5: 146 peptides, 23 chains. Longest chain 15 peptides. Score 0.448 Taking the results from Round 5 Chains 23, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 5995 restraints for refining 2622 atoms. 5526 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 11: After refmac, R = 0.1930 (Rfree = 0.000) for 2622 atoms. Found 7 (19 requested) and removed 11 (9 requested) atoms. Cycle 12: After refmac, R = 0.1782 (Rfree = 0.000) for 2610 atoms. Found 6 (19 requested) and removed 9 (9 requested) atoms. Cycle 13: After refmac, R = 0.1671 (Rfree = 0.000) for 2604 atoms. Found 4 (19 requested) and removed 11 (9 requested) atoms. Cycle 14: After refmac, R = 0.2023 (Rfree = 0.000) for 2595 atoms. Found 19 (19 requested) and removed 11 (9 requested) atoms. Cycle 15: After refmac, R = 0.2093 (Rfree = 0.000) for 2597 atoms. Found 15 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.01 3.54 Search for helices and strands: 0 residues in 0 chains, 2643 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 2663 seeds are put forward Round 1: 114 peptides, 23 chains. Longest chain 9 peptides. Score 0.291 Round 2: 149 peptides, 27 chains. Longest chain 12 peptides. Score 0.382 Round 3: 148 peptides, 25 chains. Longest chain 12 peptides. Score 0.418 Round 4: 151 peptides, 27 chains. Longest chain 12 peptides. Score 0.392 Round 5: 153 peptides, 27 chains. Longest chain 13 peptides. Score 0.401 Taking the results from Round 3 Chains 25, Residues 123, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 5759 restraints for refining 2572 atoms. 5292 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.1886 (Rfree = 0.000) for 2572 atoms. Found 15 (19 requested) and removed 9 (9 requested) atoms. Cycle 17: After refmac, R = 0.1879 (Rfree = 0.000) for 2570 atoms. Found 15 (19 requested) and removed 11 (9 requested) atoms. Cycle 18: After refmac, R = 0.1636 (Rfree = 0.000) for 2572 atoms. Found 3 (19 requested) and removed 10 (9 requested) atoms. Cycle 19: After refmac, R = 0.1580 (Rfree = 0.000) for 2563 atoms. Found 1 (19 requested) and removed 11 (9 requested) atoms. Cycle 20: After refmac, R = 0.1624 (Rfree = 0.000) for 2553 atoms. Found 6 (19 requested) and removed 11 (9 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.96 3.48 Search for helices and strands: 0 residues in 0 chains, 2625 seeds are put forward NCS extension: 11 residues added (1 deleted due to clashes), 2636 seeds are put forward Round 1: 133 peptides, 28 chains. Longest chain 8 peptides. Score 0.281 Round 2: 151 peptides, 29 chains. Longest chain 9 peptides. Score 0.351 Round 3: 132 peptides, 23 chains. Longest chain 10 peptides. Score 0.383 Round 4: 144 peptides, 24 chains. Longest chain 11 peptides. Score 0.419 Round 5: 142 peptides, 25 chains. Longest chain 12 peptides. Score 0.390 Taking the results from Round 4 Chains 24, Residues 120, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6237 restraints for refining 2691 atoms. 5781 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1752 (Rfree = 0.000) for 2691 atoms. Found 12 (20 requested) and removed 15 (10 requested) atoms. Cycle 22: After refmac, R = 0.1484 (Rfree = 0.000) for 2676 atoms. Found 12 (20 requested) and removed 11 (10 requested) atoms. Cycle 23: After refmac, R = 0.1480 (Rfree = 0.000) for 2675 atoms. Found 9 (20 requested) and removed 16 (10 requested) atoms. Cycle 24: After refmac, R = 0.1562 (Rfree = 0.000) for 2666 atoms. Found 13 (20 requested) and removed 12 (10 requested) atoms. Cycle 25: After refmac, R = 0.1476 (Rfree = 0.000) for 2663 atoms. Found 5 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.95 3.47 Search for helices and strands: 0 residues in 0 chains, 2701 seeds are put forward NCS extension: 6 residues added (0 deleted due to clashes), 2707 seeds are put forward Round 1: 120 peptides, 25 chains. Longest chain 10 peptides. Score 0.279 Round 2: 152 peptides, 28 chains. Longest chain 11 peptides. Score 0.376 Round 3: 145 peptides, 27 chains. Longest chain 8 peptides. Score 0.363 Round 4: 125 peptides, 21 chains. Longest chain 12 peptides. Score 0.391 Round 5: 130 peptides, 21 chains. Longest chain 12 peptides. Score 0.415 Taking the results from Round 5 Chains 21, Residues 109, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6323 restraints for refining 2704 atoms. 5908 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1755 (Rfree = 0.000) for 2704 atoms. Found 18 (20 requested) and removed 11 (10 requested) atoms. Cycle 27: After refmac, R = 0.1538 (Rfree = 0.000) for 2705 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 28: After refmac, R = 0.1444 (Rfree = 0.000) for 2702 atoms. Found 4 (20 requested) and removed 10 (10 requested) atoms. Cycle 29: After refmac, R = 0.1413 (Rfree = 0.000) for 2694 atoms. Found 3 (20 requested) and removed 11 (10 requested) atoms. Cycle 30: After refmac, R = 0.1400 (Rfree = 0.000) for 2686 atoms. Found 2 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.00 3.53 Search for helices and strands: 0 residues in 0 chains, 2733 seeds are put forward NCS extension: 16 residues added (2 deleted due to clashes), 2749 seeds are put forward Round 1: 128 peptides, 29 chains. Longest chain 6 peptides. Score 0.233 Round 2: 144 peptides, 29 chains. Longest chain 12 peptides. Score 0.316 Round 3: 138 peptides, 26 chains. Longest chain 8 peptides. Score 0.349 Round 4: 153 peptides, 27 chains. Longest chain 13 peptides. Score 0.401 Round 5: 163 peptides, 28 chains. Longest chain 10 peptides. Score 0.427 Taking the results from Round 5 Chains 28, Residues 135, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6247 restraints for refining 2749 atoms. 5735 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 31: After refmac, R = 0.1739 (Rfree = 0.000) for 2749 atoms. Found 15 (20 requested) and removed 16 (10 requested) atoms. Cycle 32: After refmac, R = 0.1541 (Rfree = 0.000) for 2741 atoms. Found 11 (20 requested) and removed 10 (10 requested) atoms. Cycle 33: After refmac, R = 0.1475 (Rfree = 0.000) for 2739 atoms. Found 7 (20 requested) and removed 11 (10 requested) atoms. Cycle 34: After refmac, R = 0.1460 (Rfree = 0.000) for 2733 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. Cycle 35: After refmac, R = 0.1439 (Rfree = 0.000) for 2725 atoms. Found 3 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.01 3.54 Search for helices and strands: 0 residues in 0 chains, 2773 seeds are put forward NCS extension: 4 residues added (2 deleted due to clashes), 2777 seeds are put forward Round 1: 143 peptides, 30 chains. Longest chain 7 peptides. Score 0.290 Round 2: 157 peptides, 29 chains. Longest chain 9 peptides. Score 0.380 Round 3: 144 peptides, 27 chains. Longest chain 9 peptides. Score 0.358 Round 4: 139 peptides, 23 chains. Longest chain 12 peptides. Score 0.416 Round 5: 143 peptides, 26 chains. Longest chain 13 peptides. Score 0.374 Taking the results from Round 4 Chains 23, Residues 116, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6520 restraints for refining 2768 atoms. 6079 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2058 (Rfree = 0.000) for 2768 atoms. Found 20 (20 requested) and removed 14 (10 requested) atoms. Cycle 37: After refmac, R = 0.2042 (Rfree = 0.000) for 2758 atoms. Found 20 (20 requested) and removed 13 (10 requested) atoms. Cycle 38: After refmac, R = 0.1740 (Rfree = 0.000) for 2756 atoms. Found 20 (20 requested) and removed 10 (10 requested) atoms. Cycle 39: After refmac, R = 0.1790 (Rfree = 0.000) for 2756 atoms. Found 20 (20 requested) and removed 12 (10 requested) atoms. Cycle 40: After refmac, R = 0.1233 (Rfree = 0.000) for 2758 atoms. Found 8 (20 requested) and removed 10 (10 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.98 3.51 Search for helices and strands: 0 residues in 0 chains, 2792 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 2811 seeds are put forward Round 1: 76 peptides, 17 chains. Longest chain 8 peptides. Score 0.218 Round 2: 102 peptides, 20 chains. Longest chain 10 peptides. Score 0.295 Round 3: 91 peptides, 16 chains. Longest chain 11 peptides. Score 0.329 Round 4: 93 peptides, 16 chains. Longest chain 11 peptides. Score 0.340 Round 5: 88 peptides, 14 chains. Longest chain 11 peptides. Score 0.361 Taking the results from Round 5 Chains 14, Residues 74, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 3849 reflections ( 82.76 % complete ) and 6157 restraints for refining 2605 atoms. 5859 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1735 (Rfree = 0.000) for 2605 atoms. Found 19 (19 requested) and removed 9 (9 requested) atoms. Cycle 42: After refmac, R = 0.1419 (Rfree = 0.000) for 2609 atoms. Found 19 (19 requested) and removed 10 (9 requested) atoms. Cycle 43: After refmac, R = 0.1349 (Rfree = 0.000) for 2618 atoms. Found 16 (19 requested) and removed 9 (9 requested) atoms. Cycle 44: After refmac, R = 0.1266 (Rfree = 0.000) for 2621 atoms. Found 16 (19 requested) and removed 9 (9 requested) atoms. Cycle 45: After refmac, R = 0.0968 (Rfree = 0.000) for 2626 atoms. Found 8 (19 requested) and removed 9 (9 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.01 3.54 Search for helices and strands: 0 residues in 0 chains, 2667 seeds are put forward NCS extension: 3 residues added (0 deleted due to clashes), 2670 seeds are put forward Round 1: 107 peptides, 23 chains. Longest chain 8 peptides. Score 0.253 Round 2: 118 peptides, 23 chains. Longest chain 9 peptides. Score 0.312 Round 3: 126 peptides, 24 chains. Longest chain 10 peptides. Score 0.332 Round 4: 119 peptides, 22 chains. Longest chain 9 peptides. Score 0.340 Round 5: 118 peptides, 19 chains. Longest chain 10 peptides. Score 0.400 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 99, Estimated correctness of the model 0.0 % 2 chains (10 residues) have been docked in sequence Sequence coverage is 10 % Consider running further cycles of model building using 2fqp-3_warpNtrace.pdb as input Building loops using Loopy2018 19 chains (99 residues) following loop building 2 chains (10 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3849 reflections ( 82.76 % complete ) and 5888 restraints for refining 2617 atoms. 5486 conditional restraints added. Observations/parameters ratio is 0.37 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1723 (Rfree = 0.000) for 2617 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 47: After refmac, R = 0.1415 (Rfree = 0.000) for 2605 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 48: After refmac, R = 0.1351 (Rfree = 0.000) for 2592 atoms. Found 0 (19 requested) and removed 9 (9 requested) atoms. Cycle 49: After refmac, R = 0.1335 (Rfree = 0.000) for 2582 atoms. TimeTaking 32.27