Mon 24 Dec 07:59:14 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 2hr2-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2hr2-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-4.0-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/2hr2-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-4.0-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 07:59:18 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/2hr2-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2hr2-4.0-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 865 and 0 Target number of residues in the AU: 865 Target solvent content: 0.6732 Checking the provided sequence file Detected sequence length: 159 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 6 Adjusted target number of residues: 954 Adjusted target solvent content: 0.64 Input MTZ file: 2hr2-4.0-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: 19 Cell parameters: 89.090 91.280 176.170 90.000 90.000 90.000 Input sequence file: 2hr2-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 7632 target number of atoms Had to go as low as 0.85 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: 88.085 4.000 Wilson plot Bfac: 95.09 12411 reflections ( 97.90 % complete ) and 0 restraints for refining 8462 atoms. Observations/parameters ratio is 0.37 ------------------------------------------------------ Starting model: R = 0.3383 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3701 (Rfree = 0.000) for 8462 atoms. Found 40 (40 requested) and removed 31 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.92 3.24 Search for helices and strands: 0 residues in 0 chains, 8762 seeds are put forward NCS extension: 0 residues added, 8762 seeds are put forward Round 1: 335 peptides, 54 chains. Longest chain 17 peptides. Score 0.344 Round 2: 421 peptides, 47 chains. Longest chain 26 peptides. Score 0.483 Round 3: 457 peptides, 46 chains. Longest chain 25 peptides. Score 0.525 Round 4: 475 peptides, 43 chains. Longest chain 28 peptides. Score 0.557 Round 5: 465 peptides, 42 chains. Longest chain 26 peptides. Score 0.552 Taking the results from Round 4 Chains 44, Residues 432, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15408 restraints for refining 6814 atoms. 13615 conditional restraints added. Observations/parameters ratio is 0.46 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2596 (Rfree = 0.000) for 6814 atoms. Found 32 (32 requested) and removed 42 (16 requested) atoms. Cycle 2: After refmac, R = 0.2434 (Rfree = 0.000) for 6689 atoms. Found 28 (32 requested) and removed 28 (16 requested) atoms. Cycle 3: After refmac, R = 0.2287 (Rfree = 0.000) for 6660 atoms. Found 13 (31 requested) and removed 23 (15 requested) atoms. Cycle 4: After refmac, R = 0.2260 (Rfree = 0.000) for 6630 atoms. Found 16 (31 requested) and removed 18 (15 requested) atoms. Cycle 5: After refmac, R = 0.2196 (Rfree = 0.000) for 6615 atoms. Found 9 (31 requested) and removed 27 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.86 3.19 Search for helices and strands: 0 residues in 0 chains, 7075 seeds are put forward NCS extension: 14 residues added (6 deleted due to clashes), 7089 seeds are put forward Round 1: 460 peptides, 66 chains. Longest chain 21 peptides. Score 0.428 Round 2: 483 peptides, 50 chains. Longest chain 26 peptides. Score 0.532 Round 3: 456 peptides, 48 chains. Longest chain 22 peptides. Score 0.514 Round 4: 481 peptides, 47 chains. Longest chain 32 peptides. Score 0.544 Round 5: 481 peptides, 45 chains. Longest chain 29 peptides. Score 0.553 Taking the results from Round 5 Chains 47, Residues 436, Estimated correctness of the model 0.0 % 2 chains (18 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15725 restraints for refining 6890 atoms. 13962 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2519 (Rfree = 0.000) for 6890 atoms. Found 32 (32 requested) and removed 59 (16 requested) atoms. Cycle 7: After refmac, R = 0.2526 (Rfree = 0.000) for 6782 atoms. Found 32 (32 requested) and removed 46 (16 requested) atoms. Cycle 8: After refmac, R = 0.2476 (Rfree = 0.000) for 6720 atoms. Found 32 (32 requested) and removed 58 (16 requested) atoms. Cycle 9: After refmac, R = 0.2282 (Rfree = 0.000) for 6651 atoms. Found 31 (31 requested) and removed 36 (15 requested) atoms. Cycle 10: After refmac, R = 0.2300 (Rfree = 0.000) for 6617 atoms. Found 31 (31 requested) and removed 43 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.81 3.15 Search for helices and strands: 0 residues in 0 chains, 7057 seeds are put forward NCS extension: 28 residues added (0 deleted due to clashes), 7085 seeds are put forward Round 1: 459 peptides, 76 chains. Longest chain 20 peptides. Score 0.375 Round 2: 488 peptides, 58 chains. Longest chain 27 peptides. Score 0.498 Round 3: 498 peptides, 57 chains. Longest chain 32 peptides. Score 0.513 Round 4: 498 peptides, 53 chains. Longest chain 48 peptides. Score 0.532 Round 5: 497 peptides, 52 chains. Longest chain 34 peptides. Score 0.536 Taking the results from Round 5 Chains 53, Residues 445, Estimated correctness of the model 0.0 % 2 chains (17 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15346 restraints for refining 6892 atoms. 13565 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2576 (Rfree = 0.000) for 6892 atoms. Found 32 (32 requested) and removed 70 (16 requested) atoms. Cycle 12: After refmac, R = 0.2320 (Rfree = 0.000) for 6798 atoms. Found 30 (32 requested) and removed 48 (16 requested) atoms. Cycle 13: After refmac, R = 0.2242 (Rfree = 0.000) for 6752 atoms. Found 32 (32 requested) and removed 55 (16 requested) atoms. Cycle 14: After refmac, R = 0.1824 (Rfree = 0.000) for 6710 atoms. Found 7 (31 requested) and removed 26 (15 requested) atoms. Cycle 15: After refmac, R = 0.1807 (Rfree = 0.000) for 6680 atoms. Found 7 (31 requested) and removed 23 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.82 3.15 Search for helices and strands: 0 residues in 0 chains, 7048 seeds are put forward NCS extension: 42 residues added (0 deleted due to clashes), 7090 seeds are put forward Round 1: 448 peptides, 70 chains. Longest chain 15 peptides. Score 0.394 Round 2: 482 peptides, 54 chains. Longest chain 30 peptides. Score 0.512 Round 3: 460 peptides, 59 chains. Longest chain 18 peptides. Score 0.464 Round 4: 473 peptides, 57 chains. Longest chain 29 peptides. Score 0.488 Round 5: 486 peptides, 57 chains. Longest chain 23 peptides. Score 0.501 Taking the results from Round 2 Chains 57, Residues 428, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 14932 restraints for refining 6892 atoms. 13112 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2297 (Rfree = 0.000) for 6892 atoms. Found 32 (32 requested) and removed 41 (16 requested) atoms. Cycle 17: After refmac, R = 0.2165 (Rfree = 0.000) for 6815 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 18: After refmac, R = 0.2232 (Rfree = 0.000) for 6772 atoms. Found 32 (32 requested) and removed 40 (16 requested) atoms. Cycle 19: After refmac, R = 0.1802 (Rfree = 0.000) for 6731 atoms. Found 8 (32 requested) and removed 22 (16 requested) atoms. Cycle 20: After refmac, R = 0.1764 (Rfree = 0.000) for 6698 atoms. Found 10 (31 requested) and removed 22 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.86 3.19 Search for helices and strands: 0 residues in 0 chains, 7066 seeds are put forward NCS extension: 22 residues added (3 deleted due to clashes), 7088 seeds are put forward Round 1: 436 peptides, 67 chains. Longest chain 14 peptides. Score 0.396 Round 2: 473 peptides, 63 chains. Longest chain 21 peptides. Score 0.458 Round 3: 473 peptides, 55 chains. Longest chain 24 peptides. Score 0.498 Round 4: 465 peptides, 58 chains. Longest chain 19 peptides. Score 0.474 Round 5: 478 peptides, 59 chains. Longest chain 24 peptides. Score 0.483 Taking the results from Round 3 Chains 59, Residues 418, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15286 restraints for refining 6891 atoms. 13556 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2248 (Rfree = 0.000) for 6891 atoms. Found 32 (32 requested) and removed 44 (16 requested) atoms. Cycle 22: After refmac, R = 0.2206 (Rfree = 0.000) for 6829 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 23: After refmac, R = 0.2166 (Rfree = 0.000) for 6793 atoms. Found 32 (32 requested) and removed 37 (16 requested) atoms. Cycle 24: After refmac, R = 0.1810 (Rfree = 0.000) for 6761 atoms. Found 7 (32 requested) and removed 22 (16 requested) atoms. Cycle 25: After refmac, R = 0.1788 (Rfree = 0.000) for 6736 atoms. Found 9 (32 requested) and removed 26 (16 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.87 3.20 Search for helices and strands: 0 residues in 0 chains, 7121 seeds are put forward NCS extension: 23 residues added (0 deleted due to clashes), 7144 seeds are put forward Round 1: 427 peptides, 74 chains. Longest chain 18 peptides. Score 0.347 Round 2: 457 peptides, 64 chains. Longest chain 18 peptides. Score 0.435 Round 3: 476 peptides, 64 chains. Longest chain 18 peptides. Score 0.456 Round 4: 453 peptides, 60 chains. Longest chain 19 peptides. Score 0.451 Round 5: 461 peptides, 60 chains. Longest chain 19 peptides. Score 0.460 Taking the results from Round 5 Chains 60, Residues 401, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15914 restraints for refining 6892 atoms. 14370 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2449 (Rfree = 0.000) for 6892 atoms. Found 32 (32 requested) and removed 34 (16 requested) atoms. Cycle 27: After refmac, R = 0.2263 (Rfree = 0.000) for 6846 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 28: After refmac, R = 0.2198 (Rfree = 0.000) for 6818 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 29: After refmac, R = 0.2178 (Rfree = 0.000) for 6791 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 30: After refmac, R = 0.2143 (Rfree = 0.000) for 6764 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.90 3.22 Search for helices and strands: 0 residues in 0 chains, 7198 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 7212 seeds are put forward Round 1: 385 peptides, 68 chains. Longest chain 13 peptides. Score 0.328 Round 2: 430 peptides, 67 chains. Longest chain 16 peptides. Score 0.389 Round 3: 449 peptides, 60 chains. Longest chain 21 peptides. Score 0.447 Round 4: 445 peptides, 57 chains. Longest chain 21 peptides. Score 0.458 Round 5: 433 peptides, 57 chains. Longest chain 24 peptides. Score 0.444 Taking the results from Round 4 Chains 59, Residues 388, Estimated correctness of the model 0.0 % 1 chains (10 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15823 restraints for refining 6890 atoms. 14299 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2482 (Rfree = 0.000) for 6890 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 32: After refmac, R = 0.2222 (Rfree = 0.000) for 6839 atoms. Found 32 (32 requested) and removed 23 (16 requested) atoms. Cycle 33: After refmac, R = 0.2202 (Rfree = 0.000) for 6832 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Failed to save intermediate PDB Cycle 34: After refmac, R = 0.1841 (Rfree = 0.000) for 6809 atoms. Found 7 (32 requested) and removed 28 (16 requested) atoms. Cycle 35: After refmac, R = 0.1854 (Rfree = 0.000) for 6769 atoms. Found 11 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.86 3.19 Search for helices and strands: 0 residues in 0 chains, 7131 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 7145 seeds are put forward Round 1: 393 peptides, 69 chains. Longest chain 14 peptides. Score 0.332 Round 2: 423 peptides, 62 chains. Longest chain 25 peptides. Score 0.407 Round 3: 443 peptides, 64 chains. Longest chain 14 peptides. Score 0.419 Round 4: 453 peptides, 61 chains. Longest chain 19 peptides. Score 0.446 Round 5: 424 peptides, 58 chains. Longest chain 22 peptides. Score 0.429 Taking the results from Round 4 Chains 62, Residues 392, Estimated correctness of the model 0.0 % 2 chains (22 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 15794 restraints for refining 6889 atoms. 14203 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2313 (Rfree = 0.000) for 6889 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 37: After refmac, R = 0.2316 (Rfree = 0.000) for 6852 atoms. Found 32 (32 requested) and removed 27 (16 requested) atoms. Cycle 38: After refmac, R = 0.2248 (Rfree = 0.000) for 6825 atoms. Found 32 (32 requested) and removed 32 (16 requested) atoms. Cycle 39: After refmac, R = 0.2268 (Rfree = 0.000) for 6787 atoms. Found 32 (32 requested) and removed 25 (16 requested) atoms. Cycle 40: After refmac, R = 0.2231 (Rfree = 0.000) for 6755 atoms. Found 32 (32 requested) and removed 51 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.85 3.18 Search for helices and strands: 0 residues in 0 chains, 7076 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 7095 seeds are put forward Round 1: 346 peptides, 66 chains. Longest chain 20 peptides. Score 0.288 Round 2: 395 peptides, 66 chains. Longest chain 13 peptides. Score 0.351 Round 3: 390 peptides, 61 chains. Longest chain 26 peptides. Score 0.373 Round 4: 397 peptides, 59 chains. Longest chain 22 peptides. Score 0.392 Round 5: 400 peptides, 61 chains. Longest chain 22 peptides. Score 0.385 Taking the results from Round 4 Chains 59, Residues 338, Estimated correctness of the model 0.0 % 4 chains (21 residues) have been docked in sequence ------------------------------------------------------ 12411 reflections ( 97.90 % complete ) and 16010 restraints for refining 6892 atoms. 14659 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2541 (Rfree = 0.000) for 6892 atoms. Found 32 (32 requested) and removed 43 (16 requested) atoms. Cycle 42: After refmac, R = 0.2393 (Rfree = 0.000) for 6830 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 43: After refmac, R = 0.2314 (Rfree = 0.000) for 6798 atoms. Found 32 (32 requested) and removed 35 (16 requested) atoms. Cycle 44: After refmac, R = 0.2024 (Rfree = 0.000) for 6777 atoms. Found 26 (32 requested) and removed 23 (16 requested) atoms. Cycle 45: After refmac, R = 0.2005 (Rfree = 0.000) for 6765 atoms. Found 16 (32 requested) and removed 20 (16 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.90 3.22 Search for helices and strands: 0 residues in 0 chains, 7105 seeds are put forward NCS extension: 21 residues added (4 deleted due to clashes), 7126 seeds are put forward Round 1: 342 peptides, 67 chains. Longest chain 14 peptides. Score 0.277 Round 2: 383 peptides, 58 chains. Longest chain 17 peptides. Score 0.381 Round 3: 392 peptides, 60 chains. Longest chain 17 peptides. Score 0.381 Round 4: 410 peptides, 60 chains. Longest chain 20 peptides. Score 0.402 Round 5: 403 peptides, 55 chains. Longest chain 22 peptides. Score 0.421 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 57, Residues 348, Estimated correctness of the model 0.0 % 4 chains (42 residues) have been docked in sequence Sequence coverage is 12 % Consider running further cycles of model building using 2hr2-4_warpNtrace.pdb as input Building loops using Loopy2018 57 chains (348 residues) following loop building 4 chains (42 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 12411 reflections ( 97.90 % complete ) and 15664 restraints for refining 6888 atoms. 14174 conditional restraints added. Observations/parameters ratio is 0.45 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2420 (Rfree = 0.000) for 6888 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.2330 (Rfree = 0.000) for 6825 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.2224 (Rfree = 0.000) for 6774 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.2190 (Rfree = 0.000) for 6718 atoms. TimeTaking 68.1