Mon 24 Dec 08:08:13 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 2p1a-2.1-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-2.1-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2p1a-2.1-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-2.1-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/2p1a-2.1-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-2.1-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 08:08:18 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/2p1a-2.1-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2p1a-2.1-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 276 and 0 Target number of residues in the AU: 276 Target solvent content: 0.5134 Checking the provided sequence file Detected sequence length: 154 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 308 Adjusted target solvent content: 0.46 Input MTZ file: 2p1a-2.1-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: 19 Cell parameters: 45.470 77.850 86.720 90.000 90.000 90.000 Input sequence file: 2p1a-2.1-parrot-noncs.fasta_lf Building free atoms model in initial map for 2464 target number of atoms Had to go as low as 0.45 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 1 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: 29.570 2.100 Wilson plot Bfac: 26.15 18405 reflections ( 98.93 % complete ) and 0 restraints for refining 2742 atoms. Observations/parameters ratio is 1.68 ------------------------------------------------------ Starting model: R = 0.3415 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2995 (Rfree = 0.000) for 2742 atoms. Found 50 (81 requested) and removed 50 (40 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.25 2.37 NCS extension: 0 residues added, 2742 seeds are put forward Round 1: 168 peptides, 35 chains. Longest chain 11 peptides. Score 0.323 Round 2: 169 peptides, 25 chains. Longest chain 16 peptides. Score 0.534 Round 3: 178 peptides, 24 chains. Longest chain 16 peptides. Score 0.589 Round 4: 200 peptides, 21 chains. Longest chain 26 peptides. Score 0.710 Round 5: 209 peptides, 22 chains. Longest chain 23 peptides. Score 0.723 Taking the results from Round 5 Chains 23, Residues 187, Estimated correctness of the model 92.1 % 1 chains (9 residues) have been docked in sequence ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 4882 restraints for refining 2370 atoms. 4115 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3313 (Rfree = 0.000) for 2370 atoms. Found 65 (70 requested) and removed 38 (35 requested) atoms. Cycle 2: After refmac, R = 0.3032 (Rfree = 0.000) for 2386 atoms. Found 43 (70 requested) and removed 35 (35 requested) atoms. Cycle 3: After refmac, R = 0.2882 (Rfree = 0.000) for 2386 atoms. Found 34 (68 requested) and removed 36 (35 requested) atoms. Cycle 4: After refmac, R = 0.2771 (Rfree = 0.000) for 2380 atoms. Found 33 (67 requested) and removed 20 (35 requested) atoms. Cycle 5: After refmac, R = 0.2676 (Rfree = 0.000) for 2390 atoms. Found 23 (65 requested) and removed 11 (35 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.21 2.33 NCS extension: 0 residues added, 2412 seeds are put forward Round 1: 189 peptides, 26 chains. Longest chain 15 peptides. Score 0.597 Round 2: 214 peptides, 21 chains. Longest chain 21 peptides. Score 0.748 Round 3: 206 peptides, 24 chains. Longest chain 18 peptides. Score 0.687 Round 4: 210 peptides, 22 chains. Longest chain 20 peptides. Score 0.725 Round 5: 218 peptides, 23 chains. Longest chain 22 peptides. Score 0.734 Taking the results from Round 2 Chains 21, Residues 193, Estimated correctness of the model 93.4 % 1 chains (19 residues) have been docked in sequence ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 4691 restraints for refining 2369 atoms. 3847 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2888 (Rfree = 0.000) for 2369 atoms. Found 59 (64 requested) and removed 35 (35 requested) atoms. Cycle 7: After refmac, R = 0.2735 (Rfree = 0.000) for 2391 atoms. Found 41 (64 requested) and removed 20 (35 requested) atoms. Cycle 8: After refmac, R = 0.2629 (Rfree = 0.000) for 2411 atoms. Found 21 (64 requested) and removed 12 (35 requested) atoms. Cycle 9: After refmac, R = 0.2553 (Rfree = 0.000) for 2418 atoms. Found 23 (63 requested) and removed 9 (36 requested) atoms. Cycle 10: After refmac, R = 0.2515 (Rfree = 0.000) for 2431 atoms. Found 20 (63 requested) and removed 13 (36 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.19 2.31 NCS extension: 0 residues added, 2441 seeds are put forward Round 1: 201 peptides, 19 chains. Longest chain 27 peptides. Score 0.739 Round 2: 206 peptides, 21 chains. Longest chain 25 peptides. Score 0.727 Round 3: 211 peptides, 19 chains. Longest chain 22 peptides. Score 0.765 Round 4: 210 peptides, 20 chains. Longest chain 24 peptides. Score 0.750 Round 5: 206 peptides, 19 chains. Longest chain 21 peptides. Score 0.752 Taking the results from Round 3 Chains 19, Residues 192, Estimated correctness of the model 94.1 % 2 chains (34 residues) have been docked in sequence Building loops using Loopy2018 19 chains (192 residues) following loop building 2 chains (34 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 4560 restraints for refining 2370 atoms. 3663 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2878 (Rfree = 0.000) for 2370 atoms. Found 60 (60 requested) and removed 37 (35 requested) atoms. Cycle 12: After refmac, R = 0.2732 (Rfree = 0.000) for 2392 atoms. Found 31 (60 requested) and removed 17 (35 requested) atoms. Cycle 13: After refmac, R = 0.2637 (Rfree = 0.000) for 2406 atoms. Found 30 (58 requested) and removed 12 (35 requested) atoms. Cycle 14: After refmac, R = 0.2570 (Rfree = 0.000) for 2422 atoms. Found 26 (59 requested) and removed 12 (36 requested) atoms. Cycle 15: After refmac, R = 0.2514 (Rfree = 0.000) for 2435 atoms. Found 23 (59 requested) and removed 13 (36 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.21 2.33 NCS extension: 0 residues added, 2451 seeds are put forward Round 1: 201 peptides, 21 chains. Longest chain 21 peptides. Score 0.713 Round 2: 209 peptides, 18 chains. Longest chain 26 peptides. Score 0.772 Round 3: 205 peptides, 20 chains. Longest chain 33 peptides. Score 0.737 Round 4: 211 peptides, 19 chains. Longest chain 28 peptides. Score 0.765 Round 5: 207 peptides, 14 chains. Longest chain 45 peptides. Score 0.811 Taking the results from Round 5 Chains 17, Residues 193, Estimated correctness of the model 96.1 % 3 chains (70 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 20 A and 28 A 15 chains (197 residues) following loop building 2 chains (77 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 4095 restraints for refining 2370 atoms. 3026 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 16: After refmac, R = 0.3066 (Rfree = 0.000) for 2370 atoms. Found 56 (56 requested) and removed 46 (35 requested) atoms. Cycle 17: After refmac, R = 0.2807 (Rfree = 0.000) for 2380 atoms. Found 44 (55 requested) and removed 35 (35 requested) atoms. Cycle 18: After refmac, R = 0.2688 (Rfree = 0.000) for 2388 atoms. Found 25 (54 requested) and removed 19 (35 requested) atoms. Cycle 19: After refmac, R = 0.2567 (Rfree = 0.000) for 2392 atoms. Found 20 (53 requested) and removed 12 (35 requested) atoms. Cycle 20: After refmac, R = 0.2510 (Rfree = 0.000) for 2397 atoms. Found 21 (51 requested) and removed 9 (35 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.21 2.33 NCS extension: 0 residues added, 2420 seeds are put forward Round 1: 211 peptides, 17 chains. Longest chain 40 peptides. Score 0.787 Round 2: 214 peptides, 18 chains. Longest chain 35 peptides. Score 0.783 Round 3: 217 peptides, 17 chains. Longest chain 40 peptides. Score 0.800 Round 4: 214 peptides, 23 chains. Longest chain 24 peptides. Score 0.723 Round 5: 220 peptides, 20 chains. Longest chain 46 peptides. Score 0.774 Taking the results from Round 3 Chains 19, Residues 200, Estimated correctness of the model 95.6 % 3 chains (53 residues) have been docked in sequence Building loops using Loopy2018 19 chains (200 residues) following loop building 3 chains (53 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 4177 restraints for refining 2370 atoms. 3166 conditional restraints added. Observations/parameters ratio is 1.94 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2830 (Rfree = 0.000) for 2370 atoms. Found 50 (50 requested) and removed 35 (35 requested) atoms. Cycle 22: After refmac, R = 0.2687 (Rfree = 0.000) for 2383 atoms. Found 40 (50 requested) and removed 12 (35 requested) atoms. Cycle 23: After refmac, R = 0.2598 (Rfree = 0.000) for 2407 atoms. Found 32 (50 requested) and removed 10 (35 requested) atoms. Cycle 24: After refmac, R = 0.2532 (Rfree = 0.000) for 2426 atoms. Found 26 (50 requested) and removed 17 (36 requested) atoms. Cycle 25: After refmac, R = 0.2484 (Rfree = 0.000) for 2431 atoms. Found 22 (49 requested) and removed 9 (36 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.17 2.29 NCS extension: 0 residues added, 2448 seeds are put forward Round 1: 192 peptides, 18 chains. Longest chain 28 peptides. Score 0.728 Round 2: 215 peptides, 18 chains. Longest chain 35 peptides. Score 0.785 Round 3: 212 peptides, 15 chains. Longest chain 40 peptides. Score 0.811 Round 4: 208 peptides, 20 chains. Longest chain 28 peptides. Score 0.745 Round 5: 206 peptides, 21 chains. Longest chain 16 peptides. Score 0.727 Taking the results from Round 3 Chains 18, Residues 197, Estimated correctness of the model 96.1 % 3 chains (56 residues) have been docked in sequence Building loops using Loopy2018 18 chains (197 residues) following loop building 3 chains (56 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 4289 restraints for refining 2392 atoms. 3251 conditional restraints added. Observations/parameters ratio is 1.92 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2807 (Rfree = 0.000) for 2392 atoms. Found 48 (48 requested) and removed 44 (35 requested) atoms. Cycle 27: After refmac, R = 0.2683 (Rfree = 0.000) for 2395 atoms. Found 38 (47 requested) and removed 10 (35 requested) atoms. Cycle 28: After refmac, R = 0.2597 (Rfree = 0.000) for 2419 atoms. Found 28 (48 requested) and removed 14 (36 requested) atoms. Cycle 29: After refmac, R = 0.2501 (Rfree = 0.000) for 2431 atoms. Found 23 (48 requested) and removed 14 (36 requested) atoms. Cycle 30: After refmac, R = 0.2468 (Rfree = 0.000) for 2437 atoms. Found 24 (46 requested) and removed 11 (36 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.19 2.31 NCS extension: 0 residues added, 2455 seeds are put forward Round 1: 206 peptides, 21 chains. Longest chain 26 peptides. Score 0.727 Round 2: 213 peptides, 19 chains. Longest chain 34 peptides. Score 0.769 Round 3: 210 peptides, 21 chains. Longest chain 28 peptides. Score 0.738 Round 4: 211 peptides, 19 chains. Longest chain 35 peptides. Score 0.765 Round 5: 217 peptides, 13 chains. Longest chain 72 peptides. Score 0.839 Taking the results from Round 5 Chains 14, Residues 204, Estimated correctness of the model 97.1 % 2 chains (108 residues) have been docked in sequence Building loops using Loopy2018 14 chains (204 residues) following loop building 2 chains (108 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 3853 restraints for refining 2444 atoms. 2575 conditional restraints added. Observations/parameters ratio is 1.88 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2905 (Rfree = 0.000) for 2444 atoms. Found 46 (46 requested) and removed 41 (36 requested) atoms. Cycle 32: After refmac, R = 0.2694 (Rfree = 0.000) for 2448 atoms. Found 44 (45 requested) and removed 36 (36 requested) atoms. Cycle 33: After refmac, R = 0.2583 (Rfree = 0.000) for 2453 atoms. Found 28 (44 requested) and removed 25 (36 requested) atoms. Cycle 34: After refmac, R = 0.2516 (Rfree = 0.000) for 2450 atoms. Found 24 (42 requested) and removed 12 (36 requested) atoms. Cycle 35: After refmac, R = 0.2489 (Rfree = 0.000) for 2460 atoms. Found 26 (42 requested) and removed 23 (36 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.19 2.31 NCS extension: 68 residues added (21 deleted due to clashes), 2534 seeds are put forward Round 1: 207 peptides, 18 chains. Longest chain 43 peptides. Score 0.767 Round 2: 225 peptides, 17 chains. Longest chain 78 peptides. Score 0.816 Round 3: 211 peptides, 20 chains. Longest chain 40 peptides. Score 0.753 Round 4: 214 peptides, 20 chains. Longest chain 26 peptides. Score 0.760 Round 5: 211 peptides, 18 chains. Longest chain 51 peptides. Score 0.776 Taking the results from Round 2 Chains 17, Residues 208, Estimated correctness of the model 96.3 % 1 chains (77 residues) have been docked in sequence ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 4073 restraints for refining 2402 atoms. 2896 conditional restraints added. Observations/parameters ratio is 1.92 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2766 (Rfree = 0.000) for 2402 atoms. Found 40 (40 requested) and removed 36 (35 requested) atoms. Cycle 37: After refmac, R = 0.2625 (Rfree = 0.000) for 2404 atoms. Found 36 (38 requested) and removed 14 (35 requested) atoms. Cycle 38: After refmac, R = 0.2550 (Rfree = 0.000) for 2423 atoms. Found 36 (39 requested) and removed 10 (36 requested) atoms. Cycle 39: After refmac, R = 0.2511 (Rfree = 0.000) for 2448 atoms. Found 28 (39 requested) and removed 13 (36 requested) atoms. Cycle 40: After refmac, R = 0.2476 (Rfree = 0.000) for 2463 atoms. Found 25 (39 requested) and removed 12 (36 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.22 2.34 NCS extension: 39 residues added (20 deleted due to clashes), 2518 seeds are put forward Round 1: 204 peptides, 15 chains. Longest chain 39 peptides. Score 0.794 Round 2: 215 peptides, 14 chains. Longest chain 53 peptides. Score 0.826 Round 3: 216 peptides, 15 chains. Longest chain 38 peptides. Score 0.818 Round 4: 214 peptides, 14 chains. Longest chain 54 peptides. Score 0.825 Round 5: 200 peptides, 17 chains. Longest chain 36 peptides. Score 0.762 Taking the results from Round 2 Chains 14, Residues 201, Estimated correctness of the model 96.6 % 3 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 83 A and 86 A 13 chains (203 residues) following loop building 2 chains (121 residues) in sequence following loop building ------------------------------------------------------ 18405 reflections ( 98.93 % complete ) and 3777 restraints for refining 2460 atoms. 2442 conditional restraints added. Observations/parameters ratio is 1.87 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2774 (Rfree = 0.000) for 2460 atoms. Found 39 (39 requested) and removed 39 (36 requested) atoms. Cycle 42: After refmac, R = 0.2651 (Rfree = 0.000) for 2458 atoms. Found 38 (38 requested) and removed 32 (36 requested) atoms. Cycle 43: After refmac, R = 0.2574 (Rfree = 0.000) for 2463 atoms. Found 28 (36 requested) and removed 8 (36 requested) atoms. Cycle 44: After refmac, R = 0.2509 (Rfree = 0.000) for 2481 atoms. Found 19 (37 requested) and removed 5 (37 requested) atoms. Cycle 45: After refmac, R = 0.2486 (Rfree = 0.000) for 2493 atoms. Found 23 (37 requested) and removed 16 (37 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.20 2.32 NCS extension: 30 residues added (21 deleted due to clashes), 2531 seeds are put forward Round 1: 210 peptides, 18 chains. Longest chain 42 peptides. Score 0.774 Round 2: 215 peptides, 13 chains. Longest chain 64 peptides. Score 0.836 Round 3: 213 peptides, 17 chains. Longest chain 38 peptides. Score 0.792 Round 4: 221 peptides, 15 chains. Longest chain 41 peptides. Score 0.828 Round 5: 213 peptides, 18 chains. Longest chain 24 peptides. Score 0.781 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 14, Residues 202, Estimated correctness of the model 97.0 % 3 chains (119 residues) have been docked in sequence Sequence coverage is 58 % Consider running further cycles of model building using 2p1a-2_warpNtrace.pdb as input Building loops using Loopy2018 14 chains (202 residues) following loop building 3 chains (119 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 18405 reflections ( 98.93 % complete ) and 3846 restraints for refining 2472 atoms. 2534 conditional restraints added. Observations/parameters ratio is 1.86 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2747 (Rfree = 0.000) for 2472 atoms. Found 0 (36 requested) and removed 3 (36 requested) atoms. Cycle 47: After refmac, R = 0.2628 (Rfree = 0.000) for 2468 atoms. Found 0 (36 requested) and removed 1 (36 requested) atoms. Cycle 48: After refmac, R = 0.2581 (Rfree = 0.000) for 2467 atoms. Found 0 (36 requested) and removed 0 (36 requested) atoms. Cycle 49: After refmac, R = 0.2548 (Rfree = 0.000) for 2467 atoms. TimeTaking 34.58