Mon 24 Dec 07:58:21 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 2h1q-2.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2h1q-2.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2h1q-2.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2h1q-2.0-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/2h1q-2.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2h1q-2.0-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 07:58:25 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/2h1q-2.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2h1q-2.0-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 562 and 0 Target number of residues in the AU: 562 Target solvent content: 0.5196 Checking the provided sequence file Detected sequence length: 270 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 540 Adjusted target solvent content: 0.54 Input MTZ file: 2h1q-2.0-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: 169 Cell parameters: 120.720 120.720 75.240 90.000 90.000 120.000 Input sequence file: 2h1q-2.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 4320 target number of atoms Had to go as low as 0.80 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: 28.996 2.010 Wilson plot Bfac: 27.70 40362 reflections ( 96.95 % complete ) and 0 restraints for refining 4802 atoms. Observations/parameters ratio is 2.10 ------------------------------------------------------ Starting model: R = 0.3714 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3383 (Rfree = 0.000) for 4802 atoms. Found 75 (162 requested) and removed 85 (81 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.32 2.20 NCS extension: 0 residues added, 4792 seeds are put forward Round 1: 274 peptides, 50 chains. Longest chain 15 peptides. Score 0.376 Round 2: 289 peptides, 45 chains. Longest chain 17 peptides. Score 0.466 Round 3: 306 peptides, 44 chains. Longest chain 25 peptides. Score 0.514 Round 4: 319 peptides, 39 chains. Longest chain 21 peptides. Score 0.587 Round 5: 322 peptides, 40 chains. Longest chain 24 peptides. Score 0.584 Taking the results from Round 4 Chains 41, Residues 280, Estimated correctness of the model 85.7 % 5 chains (47 residues) have been docked in sequence ------------------------------------------------------ 40362 reflections ( 96.95 % complete ) and 8339 restraints for refining 4183 atoms. 7115 conditional restraints added. Observations/parameters ratio is 2.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3492 (Rfree = 0.000) for 4183 atoms. Found 94 (141 requested) and removed 74 (70 requested) atoms. Cycle 2: After refmac, R = 0.3252 (Rfree = 0.000) for 4190 atoms. Found 73 (141 requested) and removed 52 (70 requested) atoms. Cycle 3: After refmac, R = 0.3104 (Rfree = 0.000) for 4203 atoms. Found 47 (142 requested) and removed 41 (71 requested) atoms. Failed to save intermediate PDB Cycle 4: After refmac, R = 0.3029 (Rfree = 0.000) for 4200 atoms. Found 48 (142 requested) and removed 29 (71 requested) atoms. Cycle 5: After refmac, R = 0.2952 (Rfree = 0.000) for 4216 atoms. Found 40 (142 requested) and removed 16 (71 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.21 2.10 NCS extension: 7 residues added (6 deleted due to clashes), 4261 seeds are put forward Round 1: 322 peptides, 40 chains. Longest chain 30 peptides. Score 0.584 Round 2: 322 peptides, 37 chains. Longest chain 36 peptides. Score 0.610 Round 3: 348 peptides, 43 chains. Longest chain 25 peptides. Score 0.608 Round 4: 345 peptides, 40 chains. Longest chain 24 peptides. Score 0.627 Round 5: 340 peptides, 35 chains. Longest chain 33 peptides. Score 0.659 Taking the results from Round 5 Chains 39, Residues 305, Estimated correctness of the model 90.0 % 6 chains (69 residues) have been docked in sequence ------------------------------------------------------ 40362 reflections ( 96.95 % complete ) and 8023 restraints for refining 4185 atoms. 6619 conditional restraints added. Observations/parameters ratio is 2.41 ------------------------------------------------------ Cycle 6: After refmac, R = 0.3194 (Rfree = 0.000) for 4185 atoms. Found 112 (141 requested) and removed 70 (70 requested) atoms. Cycle 7: After refmac, R = 0.3011 (Rfree = 0.000) for 4222 atoms. Found 65 (142 requested) and removed 36 (71 requested) atoms. Cycle 8: After refmac, R = 0.2874 (Rfree = 0.000) for 4247 atoms. Found 41 (143 requested) and removed 20 (71 requested) atoms. Cycle 9: After refmac, R = 0.2785 (Rfree = 0.000) for 4265 atoms. Found 29 (144 requested) and removed 12 (72 requested) atoms. Cycle 10: After refmac, R = 0.2732 (Rfree = 0.000) for 4280 atoms. Found 19 (144 requested) and removed 14 (72 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.16 2.05 NCS extension: 30 residues added (1 deleted due to clashes), 4325 seeds are put forward Round 1: 325 peptides, 34 chains. Longest chain 30 peptides. Score 0.641 Round 2: 344 peptides, 30 chains. Longest chain 36 peptides. Score 0.703 Round 3: 346 peptides, 33 chains. Longest chain 35 peptides. Score 0.684 Round 4: 355 peptides, 32 chains. Longest chain 36 peptides. Score 0.705 Round 5: 352 peptides, 34 chains. Longest chain 41 peptides. Score 0.686 Taking the results from Round 4 Chains 39, Residues 323, Estimated correctness of the model 92.3 % 7 chains (119 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 40 B and 46 B 35 chains (324 residues) following loop building 6 chains (124 residues) in sequence following loop building ------------------------------------------------------ 40362 reflections ( 96.95 % complete ) and 7275 restraints for refining 4212 atoms. 5584 conditional restraints added. Observations/parameters ratio is 2.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.3047 (Rfree = 0.000) for 4212 atoms. Found 105 (142 requested) and removed 77 (71 requested) atoms. Cycle 12: After refmac, R = 0.2891 (Rfree = 0.000) for 4238 atoms. Found 51 (140 requested) and removed 35 (71 requested) atoms. Cycle 13: After refmac, R = 0.2794 (Rfree = 0.000) for 4250 atoms. Found 62 (137 requested) and removed 18 (71 requested) atoms. Cycle 14: After refmac, R = 0.2714 (Rfree = 0.000) for 4292 atoms. Found 47 (139 requested) and removed 10 (72 requested) atoms. Failed to save intermediate PDB Cycle 15: After refmac, R = 0.2672 (Rfree = 0.000) for 4325 atoms. Found 25 (140 requested) and removed 16 (73 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.17 2.06 NCS extension: 0 residues added, 4346 seeds are put forward Round 1: 342 peptides, 31 chains. Longest chain 59 peptides. Score 0.692 Round 2: 350 peptides, 28 chains. Longest chain 45 peptides. Score 0.726 Round 3: 339 peptides, 29 chains. Longest chain 40 peptides. Score 0.703 Round 4: 339 peptides, 28 chains. Longest chain 44 peptides. Score 0.710 Round 5: 341 peptides, 26 chains. Longest chain 45 peptides. Score 0.727 Taking the results from Round 5 Chains 29, Residues 315, Estimated correctness of the model 93.3 % 9 chains (190 residues) have been docked in sequence Building loops using Loopy2018 29 chains (315 residues) following loop building 9 chains (190 residues) in sequence following loop building ------------------------------------------------------ 40362 reflections ( 96.95 % complete ) and 6777 restraints for refining 4261 atoms. 4842 conditional restraints added. Observations/parameters ratio is 2.37 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2959 (Rfree = 0.000) for 4261 atoms. Found 116 (134 requested) and removed 77 (71 requested) atoms. Cycle 17: After refmac, R = 0.2791 (Rfree = 0.000) for 4299 atoms. Found 51 (133 requested) and removed 31 (72 requested) atoms. Cycle 18: After refmac, R = 0.2701 (Rfree = 0.000) for 4314 atoms. Found 45 (130 requested) and removed 19 (72 requested) atoms. Cycle 19: After refmac, R = 0.2653 (Rfree = 0.000) for 4338 atoms. Found 43 (131 requested) and removed 14 (73 requested) atoms. Cycle 20: After refmac, R = 0.2600 (Rfree = 0.000) for 4362 atoms. Found 37 (132 requested) and removed 15 (73 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.18 2.07 NCS extension: 20 residues added (15 deleted due to clashes), 4409 seeds are put forward Round 1: 323 peptides, 28 chains. Longest chain 42 peptides. Score 0.685 Round 2: 337 peptides, 25 chains. Longest chain 45 peptides. Score 0.728 Round 3: 343 peptides, 25 chains. Longest chain 43 peptides. Score 0.737 Round 4: 340 peptides, 26 chains. Longest chain 39 peptides. Score 0.726 Round 5: 339 peptides, 27 chains. Longest chain 40 peptides. Score 0.717 Taking the results from Round 3 Chains 35, Residues 318, Estimated correctness of the model 93.8 % 8 chains (173 residues) have been docked in sequence Building loops using Loopy2018 35 chains (318 residues) following loop building 8 chains (173 residues) in sequence following loop building ------------------------------------------------------ 40362 reflections ( 96.95 % complete ) and 7006 restraints for refining 4280 atoms. 5133 conditional restraints added. Observations/parameters ratio is 2.36 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2839 (Rfree = 0.000) for 4280 atoms. Found 103 (130 requested) and removed 67 (72 requested) atoms. Cycle 22: After refmac, R = 0.2718 (Rfree = 0.000) for 4315 atoms. Found 71 (128 requested) and removed 11 (72 requested) atoms. Cycle 23: After refmac, R = 0.2631 (Rfree = 0.000) for 4371 atoms. Found 40 (129 requested) and removed 15 (73 requested) atoms. Cycle 24: After refmac, R = 0.2579 (Rfree = 0.000) for 4392 atoms. Found 39 (130 requested) and removed 10 (74 requested) atoms. Cycle 25: After refmac, R = 0.2530 (Rfree = 0.000) for 4416 atoms. Found 28 (131 requested) and removed 9 (74 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.16 2.05 NCS extension: 3 residues added (3 deleted due to clashes), 4443 seeds are put forward Round 1: 346 peptides, 30 chains. Longest chain 46 peptides. Score 0.706 Round 2: 343 peptides, 26 chains. Longest chain 47 peptides. Score 0.730 Round 3: 344 peptides, 24 chains. Longest chain 38 peptides. Score 0.745 Round 4: 346 peptides, 26 chains. Longest chain 38 peptides. Score 0.734 Round 5: 336 peptides, 27 chains. Longest chain 45 peptides. Score 0.713 Taking the results from Round 3 Chains 30, Residues 320, Estimated correctness of the model 94.1 % 8 chains (165 residues) have been docked in sequence Building loops using Loopy2018 30 chains (320 residues) following loop building 8 chains (165 residues) in sequence following loop building ------------------------------------------------------ 40362 reflections ( 96.95 % complete ) and 7139 restraints for refining 4330 atoms. 5295 conditional restraints added. Observations/parameters ratio is 2.33 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2772 (Rfree = 0.000) for 4330 atoms. Found 112 (128 requested) and removed 59 (73 requested) atoms. Cycle 27: After refmac, R = 0.2645 (Rfree = 0.000) for 4382 atoms. Found 57 (127 requested) and removed 12 (74 requested) atoms. Cycle 28: After refmac, R = 0.2563 (Rfree = 0.000) for 4422 atoms. Found 41 (128 requested) and removed 15 (74 requested) atoms. Cycle 29: After refmac, R = 0.2515 (Rfree = 0.000) for 4443 atoms. Found 40 (129 requested) and removed 8 (75 requested) atoms. Cycle 30: After refmac, R = 0.2476 (Rfree = 0.000) for 4473 atoms. Found 31 (130 requested) and removed 10 (75 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.15 2.04 NCS extension: 12 residues added (24 deleted due to clashes), 4514 seeds are put forward Round 1: 332 peptides, 26 chains. Longest chain 42 peptides. Score 0.714 Round 2: 337 peptides, 25 chains. Longest chain 38 peptides. Score 0.728 Round 3: 344 peptides, 29 chains. Longest chain 37 peptides. Score 0.710 Round 4: 347 peptides, 28 chains. Longest chain 38 peptides. Score 0.721 Round 5: 345 peptides, 25 chains. Longest chain 52 peptides. Score 0.739 Taking the results from Round 5 Chains 26, Residues 320, Estimated correctness of the model 93.8 % 6 chains (183 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 194 B and 204 B 24 chains (325 residues) following loop building 5 chains (192 residues) in sequence following loop building ------------------------------------------------------ 40362 reflections ( 96.95 % complete ) and 6884 restraints for refining 4401 atoms. 4885 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2799 (Rfree = 0.000) for 4401 atoms. Found 119 (127 requested) and removed 82 (74 requested) atoms. Cycle 32: After refmac, R = 0.2642 (Rfree = 0.000) for 4435 atoms. Found 62 (125 requested) and removed 16 (74 requested) atoms. Cycle 33: After refmac, R = 0.2535 (Rfree = 0.000) for 4477 atoms. Found 44 (127 requested) and removed 13 (75 requested) atoms. Cycle 34: After refmac, R = 0.2473 (Rfree = 0.000) for 4502 atoms. Found 46 (128 requested) and removed 8 (76 requested) atoms. Cycle 35: After refmac, R = 0.2424 (Rfree = 0.000) for 4533 atoms. Found 27 (129 requested) and removed 11 (76 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.18 2.07 NCS extension: 7 residues added (37 deleted due to clashes), 4564 seeds are put forward Round 1: 336 peptides, 28 chains. Longest chain 42 peptides. Score 0.705 Round 2: 353 peptides, 28 chains. Longest chain 44 peptides. Score 0.730 Round 3: 356 peptides, 28 chains. Longest chain 44 peptides. Score 0.734 Round 4: 351 peptides, 27 chains. Longest chain 51 peptides. Score 0.734 Round 5: 347 peptides, 25 chains. Longest chain 44 peptides. Score 0.742 Taking the results from Round 5 Chains 28, Residues 322, Estimated correctness of the model 94.0 % 8 chains (200 residues) have been docked in sequence Building loops using Loopy2018 28 chains (322 residues) following loop building 8 chains (200 residues) in sequence following loop building ------------------------------------------------------ 40362 reflections ( 96.95 % complete ) and 6810 restraints for refining 4408 atoms. 4805 conditional restraints added. Observations/parameters ratio is 2.29 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2696 (Rfree = 0.000) for 4408 atoms. Found 113 (124 requested) and removed 62 (74 requested) atoms. Cycle 37: After refmac, R = 0.2567 (Rfree = 0.000) for 4452 atoms. Found 59 (123 requested) and removed 20 (75 requested) atoms. Cycle 38: After refmac, R = 0.2485 (Rfree = 0.000) for 4486 atoms. Found 42 (124 requested) and removed 14 (75 requested) atoms. Cycle 39: After refmac, R = 0.2425 (Rfree = 0.000) for 4511 atoms. Found 43 (125 requested) and removed 14 (76 requested) atoms. Cycle 40: After refmac, R = 0.2397 (Rfree = 0.000) for 4537 atoms. Found 30 (125 requested) and removed 17 (76 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.18 2.07 NCS extension: 13 residues added (8 deleted due to clashes), 4567 seeds are put forward Round 1: 344 peptides, 32 chains. Longest chain 49 peptides. Score 0.688 Round 2: 349 peptides, 23 chains. Longest chain 62 peptides. Score 0.758 Round 3: 346 peptides, 24 chains. Longest chain 62 peptides. Score 0.747 Round 4: 359 peptides, 29 chains. Longest chain 45 peptides. Score 0.731 Round 5: 343 peptides, 25 chains. Longest chain 48 peptides. Score 0.737 Taking the results from Round 2 Chains 26, Residues 326, Estimated correctness of the model 94.6 % 8 chains (206 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 42 B and 48 B Built loop between residues 58 B and 69 B 22 chains (338 residues) following loop building 6 chains (221 residues) in sequence following loop building ------------------------------------------------------ 40362 reflections ( 96.95 % complete ) and 6746 restraints for refining 4514 atoms. 4589 conditional restraints added. Observations/parameters ratio is 2.24 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2650 (Rfree = 0.000) for 4514 atoms. Found 118 (122 requested) and removed 78 (76 requested) atoms. Cycle 42: After refmac, R = 0.2526 (Rfree = 0.000) for 4552 atoms. Found 68 (119 requested) and removed 16 (76 requested) atoms. Cycle 43: After refmac, R = 0.2442 (Rfree = 0.000) for 4600 atoms. Found 49 (121 requested) and removed 25 (77 requested) atoms. Cycle 44: After refmac, R = 0.2369 (Rfree = 0.000) for 4620 atoms. Found 43 (119 requested) and removed 17 (78 requested) atoms. Cycle 45: After refmac, R = 0.2328 (Rfree = 0.000) for 4642 atoms. Found 48 (119 requested) and removed 10 (78 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.17 2.06 NCS extension: 56 residues added (44 deleted due to clashes), 4739 seeds are put forward Round 1: 335 peptides, 25 chains. Longest chain 45 peptides. Score 0.725 Round 2: 351 peptides, 22 chains. Longest chain 67 peptides. Score 0.767 Round 3: 350 peptides, 23 chains. Longest chain 48 peptides. Score 0.759 Round 4: 339 peptides, 28 chains. Longest chain 44 peptides. Score 0.710 Round 5: 334 peptides, 23 chains. Longest chain 39 peptides. Score 0.738 Taking the results from Round 2 Last building cycle: Chain fragments will be rearranged Chains 24, Residues 329, Estimated correctness of the model 95.0 % 7 chains (225 residues) have been docked in sequence Sequence coverage is 68 % Consider running further cycles of model building using 2h1q-2_warpNtrace.pdb as input Building loops using Loopy2018 Built loop between residues 59 B and 67 B Built loop between residues 226 B and 230 B 22 chains (339 residues) following loop building 5 chains (235 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 40362 reflections ( 96.95 % complete ) and 6693 restraints for refining 4595 atoms. 4472 conditional restraints added. Observations/parameters ratio is 2.20 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2593 (Rfree = 0.000) for 4595 atoms. Found 0 (118 requested) and removed 6 (77 requested) atoms. Cycle 47: After refmac, R = 0.2507 (Rfree = 0.000) for 4584 atoms. Found 0 (114 requested) and removed 0 (77 requested) atoms. Cycle 48: After refmac, R = 0.2466 (Rfree = 0.000) for 4581 atoms. Found 0 (114 requested) and removed 3 (77 requested) atoms. Cycle 49: After refmac, R = 0.2448 (Rfree = 0.000) for 4576 atoms. TimeTaking 53.65