Mon 24 Dec 07:43:46 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 2opk-2.1-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2opk-2.1-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2opk-2.1-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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/2opk-2.1-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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 07:43:51 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/2opk-2.1-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2opk-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 592 and 0 Target number of residues in the AU: 592 Target solvent content: 0.4361 Checking the provided sequence file Detected sequence length: 112 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 4 Adjusted target number of residues: 448 Adjusted target solvent content: 0.57 Input MTZ file: 2opk-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: 96 Cell parameters: 75.570 75.570 198.970 90.000 90.000 90.000 Input sequence file: 2opk-2.1-parrot-noncs.fasta_lf Building free atoms model in initial map for 3584 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 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: 28.177 2.101 Wilson plot Bfac: 12.57 34444 reflections ( 99.66 % complete ) and 0 restraints for refining 3980 atoms. Observations/parameters ratio is 2.16 ------------------------------------------------------ Starting model: R = 0.3229 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2860 (Rfree = 0.000) for 3980 atoms. Found 100 (118 requested) and removed 63 (59 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.97 1.79 NCS extension: 0 residues added, 4017 seeds are put forward Round 1: 320 peptides, 39 chains. Longest chain 19 peptides. Score 0.620 Round 2: 344 peptides, 29 chains. Longest chain 37 peptides. Score 0.743 Round 3: 360 peptides, 22 chains. Longest chain 51 peptides. Score 0.809 Round 4: 382 peptides, 21 chains. Longest chain 42 peptides. Score 0.837 Round 5: 399 peptides, 15 chains. Longest chain 55 peptides. Score 0.880 Taking the results from Round 5 Chains 16, Residues 384, Estimated correctness of the model 98.3 % 8 chains (317 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 68 C and 72 C Built loop between residues 67 B and 72 B Built loop between residues 68 D and 72 D 13 chains (394 residues) following loop building 5 chains (327 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4584 restraints for refining 3868 atoms. 1679 conditional restraints added. Observations/parameters ratio is 2.23 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3144 (Rfree = 0.000) for 3868 atoms. Found 115 (115 requested) and removed 63 (57 requested) atoms. Cycle 2: After refmac, R = 0.2952 (Rfree = 0.000) for 3912 atoms. Found 98 (114 requested) and removed 27 (58 requested) atoms. Cycle 3: After refmac, R = 0.2837 (Rfree = 0.000) for 3977 atoms. Found 84 (116 requested) and removed 26 (59 requested) atoms. Cycle 4: After refmac, R = 0.2695 (Rfree = 0.000) for 4031 atoms. Found 81 (118 requested) and removed 25 (60 requested) atoms. Cycle 5: After refmac, R = 0.2616 (Rfree = 0.000) for 4070 atoms. Found 98 (119 requested) and removed 21 (60 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.83 1.67 NCS extension: 5 residues added (40 deleted due to clashes), 4155 seeds are put forward Round 1: 409 peptides, 11 chains. Longest chain 67 peptides. Score 0.903 Round 2: 410 peptides, 11 chains. Longest chain 106 peptides. Score 0.904 Round 3: 409 peptides, 11 chains. Longest chain 61 peptides. Score 0.903 Round 4: 411 peptides, 12 chains. Longest chain 66 peptides. Score 0.900 Round 5: 418 peptides, 9 chains. Longest chain 107 peptides. Score 0.916 Taking the results from Round 5 Chains 11, Residues 409, Estimated correctness of the model 99.1 % 9 chains (407 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 27 A and 30 A Built loop between residues 78 A and 81 A Built loop between residues 46 C and 49 C Built loop between residues 68 C and 72 C Built loop between residues 68 D and 75 D 6 chains (424 residues) following loop building 4 chains (422 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4068 restraints for refining 4056 atoms. 669 conditional restraints added. Observations/parameters ratio is 2.12 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2716 (Rfree = 0.000) for 4056 atoms. Found 118 (118 requested) and removed 63 (60 requested) atoms. Cycle 7: After refmac, R = 0.2592 (Rfree = 0.000) for 4102 atoms. Found 105 (117 requested) and removed 19 (61 requested) atoms. Cycle 8: After refmac, R = 0.2498 (Rfree = 0.000) for 4175 atoms. Found 83 (119 requested) and removed 28 (62 requested) atoms. Cycle 9: After refmac, R = 0.2419 (Rfree = 0.000) for 4222 atoms. Found 72 (120 requested) and removed 29 (62 requested) atoms. Cycle 10: After refmac, R = 0.2368 (Rfree = 0.000) for 4248 atoms. Found 69 (121 requested) and removed 20 (63 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.80 1.64 NCS extension: 8 residues added (80 deleted due to clashes), 4309 seeds are put forward Round 1: 414 peptides, 8 chains. Longest chain 83 peptides. Score 0.917 Round 2: 409 peptides, 9 chains. Longest chain 78 peptides. Score 0.911 Round 3: 418 peptides, 8 chains. Longest chain 109 peptides. Score 0.919 Round 4: 418 peptides, 7 chains. Longest chain 104 peptides. Score 0.923 Round 5: 413 peptides, 12 chains. Longest chain 79 peptides. Score 0.902 Taking the results from Round 4 Chains 8, Residues 411, Estimated correctness of the model 99.2 % 7 chains (407 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 29 A and 35 A Built loop between residues 68 C and 75 C Built loop between residues 68 B and 71 B 4 chains (420 residues) following loop building 4 chains (420 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4123 restraints for refining 4142 atoms. 742 conditional restraints added. Observations/parameters ratio is 2.08 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2552 (Rfree = 0.000) for 4142 atoms. Found 118 (118 requested) and removed 37 (61 requested) atoms. Cycle 12: After refmac, R = 0.2417 (Rfree = 0.000) for 4216 atoms. Found 83 (120 requested) and removed 21 (62 requested) atoms. Cycle 13: After refmac, R = 0.2334 (Rfree = 0.000) for 4269 atoms. Found 74 (122 requested) and removed 23 (63 requested) atoms. Cycle 14: After refmac, R = 0.2285 (Rfree = 0.000) for 4312 atoms. Found 83 (123 requested) and removed 22 (64 requested) atoms. Cycle 15: After refmac, R = 0.2262 (Rfree = 0.000) for 4364 atoms. Found 82 (125 requested) and removed 25 (65 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.76 1.60 NCS extension: 5 residues added (39 deleted due to clashes), 4429 seeds are put forward Round 1: 420 peptides, 6 chains. Longest chain 110 peptides. Score 0.927 Round 2: 424 peptides, 4 chains. Longest chain 110 peptides. Score 0.936 Round 3: 421 peptides, 9 chains. Longest chain 98 peptides. Score 0.917 Round 4: 425 peptides, 8 chains. Longest chain 110 peptides. Score 0.923 Round 5: 422 peptides, 5 chains. Longest chain 110 peptides. Score 0.932 Taking the results from Round 2 Chains 4, Residues 420, Estimated correctness of the model 99.5 % 4 chains (420 residues) have been docked in sequence Building loops using Loopy2018 4 chains (420 residues) following loop building 4 chains (420 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4208 restraints for refining 4211 atoms. 838 conditional restraints added. Observations/parameters ratio is 2.04 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2342 (Rfree = 0.000) for 4211 atoms. Found 120 (120 requested) and removed 38 (62 requested) atoms. Cycle 17: After refmac, R = 0.2280 (Rfree = 0.000) for 4286 atoms. Found 68 (122 requested) and removed 25 (63 requested) atoms. Cycle 18: After refmac, R = 0.2234 (Rfree = 0.000) for 4327 atoms. Found 63 (123 requested) and removed 24 (64 requested) atoms. Cycle 19: After refmac, R = 0.2211 (Rfree = 0.000) for 4359 atoms. Found 77 (124 requested) and removed 36 (64 requested) atoms. Cycle 20: After refmac, R = 0.2197 (Rfree = 0.000) for 4393 atoms. Found 67 (125 requested) and removed 45 (65 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.76 1.60 NCS extension: 5 residues added (1 deleted due to clashes), 4420 seeds are put forward Round 1: 418 peptides, 8 chains. Longest chain 83 peptides. Score 0.919 Round 2: 421 peptides, 6 chains. Longest chain 104 peptides. Score 0.928 Round 3: 418 peptides, 9 chains. Longest chain 104 peptides. Score 0.916 Round 4: 419 peptides, 8 chains. Longest chain 110 peptides. Score 0.920 Round 5: 422 peptides, 8 chains. Longest chain 110 peptides. Score 0.921 Taking the results from Round 2 Chains 7, Residues 415, Estimated correctness of the model 99.3 % 6 chains (413 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 71 A and 74 A Built loop between residues 68 D and 71 D 5 chains (419 residues) following loop building 4 chains (417 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4219 restraints for refining 4207 atoms. 863 conditional restraints added. Observations/parameters ratio is 2.05 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2307 (Rfree = 0.000) for 4207 atoms. Found 117 (117 requested) and removed 48 (62 requested) atoms. Cycle 22: After refmac, R = 0.2238 (Rfree = 0.000) for 4271 atoms. Found 96 (119 requested) and removed 26 (63 requested) atoms. Cycle 23: After refmac, R = 0.2200 (Rfree = 0.000) for 4333 atoms. Found 79 (121 requested) and removed 27 (64 requested) atoms. Cycle 24: After refmac, R = 0.2162 (Rfree = 0.000) for 4381 atoms. Found 67 (122 requested) and removed 26 (65 requested) atoms. Cycle 25: After refmac, R = 0.2133 (Rfree = 0.000) for 4419 atoms. Found 63 (123 requested) and removed 32 (65 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.76 1.60 NCS extension: 5 residues added (0 deleted due to clashes), 4457 seeds are put forward Round 1: 423 peptides, 6 chains. Longest chain 107 peptides. Score 0.929 Round 2: 427 peptides, 4 chains. Longest chain 110 peptides. Score 0.937 Round 3: 421 peptides, 9 chains. Longest chain 110 peptides. Score 0.917 Round 4: 431 peptides, 4 chains. Longest chain 110 peptides. Score 0.939 Round 5: 424 peptides, 8 chains. Longest chain 110 peptides. Score 0.922 Taking the results from Round 4 Chains 4, Residues 427, Estimated correctness of the model 99.5 % 4 chains (427 residues) have been docked in sequence Building loops using Loopy2018 4 chains (427 residues) following loop building 4 chains (427 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4141 restraints for refining 4233 atoms. 714 conditional restraints added. Observations/parameters ratio is 2.03 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2283 (Rfree = 0.000) for 4233 atoms. Found 116 (116 requested) and removed 39 (63 requested) atoms. Cycle 27: After refmac, R = 0.2215 (Rfree = 0.000) for 4306 atoms. Found 111 (118 requested) and removed 28 (64 requested) atoms. Cycle 28: After refmac, R = 0.2168 (Rfree = 0.000) for 4389 atoms. Found 73 (120 requested) and removed 39 (65 requested) atoms. Cycle 29: After refmac, R = 0.2175 (Rfree = 0.000) for 4418 atoms. Found 71 (118 requested) and removed 25 (65 requested) atoms. Cycle 30: After refmac, R = 0.2180 (Rfree = 0.000) for 4461 atoms. Found 62 (119 requested) and removed 44 (66 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.76 1.60 NCS extension: 10 residues added (78 deleted due to clashes), 4492 seeds are put forward Round 1: 424 peptides, 6 chains. Longest chain 107 peptides. Score 0.929 Round 2: 425 peptides, 4 chains. Longest chain 110 peptides. Score 0.936 Round 3: 425 peptides, 7 chains. Longest chain 110 peptides. Score 0.926 Round 4: 423 peptides, 8 chains. Longest chain 110 peptides. Score 0.922 Round 5: 423 peptides, 9 chains. Longest chain 101 peptides. Score 0.918 Taking the results from Round 2 Chains 4, Residues 421, Estimated correctness of the model 99.5 % 4 chains (421 residues) have been docked in sequence Building loops using Loopy2018 4 chains (421 residues) following loop building 4 chains (421 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4257 restraints for refining 4308 atoms. 873 conditional restraints added. Observations/parameters ratio is 2.00 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2363 (Rfree = 0.000) for 4308 atoms. Found 113 (113 requested) and removed 42 (64 requested) atoms. Cycle 32: After refmac, R = 0.2304 (Rfree = 0.000) for 4376 atoms. Found 80 (114 requested) and removed 21 (65 requested) atoms. Cycle 33: After refmac, R = 0.2272 (Rfree = 0.000) for 4431 atoms. Found 67 (115 requested) and removed 16 (65 requested) atoms. Cycle 34: After refmac, R = 0.2250 (Rfree = 0.000) for 4481 atoms. Found 54 (117 requested) and removed 22 (66 requested) atoms. Cycle 35: After refmac, R = 0.2231 (Rfree = 0.000) for 4507 atoms. Found 64 (118 requested) and removed 26 (67 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.77 1.61 NCS extension: 4 residues added (46 deleted due to clashes), 4552 seeds are put forward Round 1: 420 peptides, 5 chains. Longest chain 106 peptides. Score 0.931 Round 2: 422 peptides, 4 chains. Longest chain 107 peptides. Score 0.935 Round 3: 419 peptides, 9 chains. Longest chain 107 peptides. Score 0.916 Round 4: 421 peptides, 8 chains. Longest chain 107 peptides. Score 0.921 Round 5: 425 peptides, 8 chains. Longest chain 83 peptides. Score 0.923 Taking the results from Round 2 Chains 4, Residues 418, Estimated correctness of the model 99.4 % 4 chains (418 residues) have been docked in sequence Building loops using Loopy2018 4 chains (418 residues) following loop building 4 chains (418 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4366 restraints for refining 4348 atoms. 1003 conditional restraints added. Observations/parameters ratio is 1.98 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2378 (Rfree = 0.000) for 4348 atoms. Found 114 (114 requested) and removed 39 (64 requested) atoms. Cycle 37: After refmac, R = 0.2312 (Rfree = 0.000) for 4420 atoms. Found 75 (115 requested) and removed 16 (65 requested) atoms. Cycle 38: After refmac, R = 0.2276 (Rfree = 0.000) for 4477 atoms. Found 54 (117 requested) and removed 14 (66 requested) atoms. Cycle 39: After refmac, R = 0.2244 (Rfree = 0.000) for 4512 atoms. Found 59 (118 requested) and removed 18 (67 requested) atoms. Cycle 40: After refmac, R = 0.2227 (Rfree = 0.000) for 4547 atoms. Found 62 (119 requested) and removed 15 (67 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.76 1.60 NCS extension: 8 residues added (78 deleted due to clashes), 4604 seeds are put forward Round 1: 423 peptides, 5 chains. Longest chain 109 peptides. Score 0.932 Round 2: 420 peptides, 8 chains. Longest chain 104 peptides. Score 0.920 Round 3: 423 peptides, 6 chains. Longest chain 110 peptides. Score 0.929 Round 4: 418 peptides, 9 chains. Longest chain 110 peptides. Score 0.916 Round 5: 423 peptides, 8 chains. Longest chain 75 peptides. Score 0.922 Taking the results from Round 1 Chains 5, Residues 418, Estimated correctness of the model 99.4 % 5 chains (418 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 69 B and 72 B 4 chains (420 residues) following loop building 4 chains (420 residues) in sequence following loop building ------------------------------------------------------ 34444 reflections ( 99.66 % complete ) and 4391 restraints for refining 4390 atoms. 1011 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2367 (Rfree = 0.000) for 4390 atoms. Found 114 (114 requested) and removed 35 (65 requested) atoms. Cycle 42: After refmac, R = 0.2319 (Rfree = 0.000) for 4468 atoms. Found 89 (116 requested) and removed 14 (66 requested) atoms. Cycle 43: After refmac, R = 0.2284 (Rfree = 0.000) for 4542 atoms. Found 64 (119 requested) and removed 22 (67 requested) atoms. Cycle 44: After refmac, R = 0.2254 (Rfree = 0.000) for 4580 atoms. Found 58 (120 requested) and removed 29 (68 requested) atoms. Cycle 45: After refmac, R = 0.2230 (Rfree = 0.000) for 4604 atoms. Found 56 (121 requested) and removed 22 (68 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.76 1.60 NCS extension: 8 residues added (43 deleted due to clashes), 4647 seeds are put forward Round 1: 419 peptides, 6 chains. Longest chain 109 peptides. Score 0.927 Round 2: 415 peptides, 9 chains. Longest chain 104 peptides. Score 0.914 Round 3: 426 peptides, 6 chains. Longest chain 110 peptides. Score 0.930 Round 4: 421 peptides, 7 chains. Longest chain 110 peptides. Score 0.924 Round 5: 424 peptides, 7 chains. Longest chain 110 peptides. Score 0.926 Taking the results from Round 3 Last building cycle: Chain fragments will be rearranged Chains 6, Residues 420, Estimated correctness of the model 99.4 % 6 chains (420 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 32 C and 35 C Built loop between residues 68 B and 72 B 4 chains (425 residues) following loop building 4 chains (425 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 34444 reflections ( 99.66 % complete ) and 3414 restraints for refining 3301 atoms. Observations/parameters ratio is 2.61 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2801 (Rfree = 0.000) for 3301 atoms. Found 42 (86 requested) and removed 0 (86 requested) atoms. Cycle 47: After refmac, R = 0.2640 (Rfree = 0.000) for 3301 atoms. Found 7 (87 requested) and removed 0 (49 requested) atoms. Failed to save intermediate PDB Cycle 48: After refmac, R = 0.2567 (Rfree = 0.000) for 3301 atoms. Found 10 (87 requested) and removed 0 (49 requested) atoms. Cycle 49: After refmac, R = 0.2519 (Rfree = 0.000) for 3301 atoms. TimeTaking 63.85