Mon 24 Dec 08:08:22 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 2ich-4.0-parrot-noncs X-ray data file /users/emra500/scratch/Dataset/noncsChltofom/2ich-4.0-parrot-noncs.mtz Sequence file /users/emra500/scratch/Dataset/noncsChltofom/2ich-4.0-parrot-noncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-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/2ich-4.0-parrot-noncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-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 08:08:26 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/2ich-4.0-parrot-noncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/noncs/ArpWArp/wArpResults/WorkingDir/2ich-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 510 and 0 Target number of residues in the AU: 510 Target solvent content: 0.6251 Checking the provided sequence file Detected sequence length: 335 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 670 Adjusted target solvent content: 0.51 Input MTZ file: 2ich-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: 63.275 95.573 121.745 90.000 90.000 90.000 Input sequence file: 2ich-4.0-parrot-noncs.fasta_lf Building free atoms model in initial map for 5360 target number of atoms Had to go as low as 0.70 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: 29.160 4.000 Wilson plot Bfac: 63.72 6601 reflections ( 99.58 % complete ) and 0 restraints for refining 5901 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.3241 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3112 (Rfree = 0.000) for 5901 atoms. Found 28 (28 requested) and removed 43 (14 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.54 3.49 Search for helices and strands: 0 residues in 0 chains, 5950 seeds are put forward NCS extension: 0 residues added, 5950 seeds are put forward Round 1: 242 peptides, 49 chains. Longest chain 9 peptides. Score 0.287 Round 2: 331 peptides, 56 chains. Longest chain 14 peptides. Score 0.422 Round 3: 338 peptides, 52 chains. Longest chain 20 peptides. Score 0.472 Round 4: 355 peptides, 48 chains. Longest chain 17 peptides. Score 0.539 Round 5: 369 peptides, 46 chains. Longest chain 29 peptides. Score 0.579 Taking the results from Round 5 Chains 46, Residues 323, Estimated correctness of the model 0.0 % 1 chains (8 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11161 restraints for refining 4840 atoms. 9889 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2705 (Rfree = 0.000) for 4840 atoms. Found 23 (23 requested) and removed 53 (11 requested) atoms. Cycle 2: After refmac, R = 0.2419 (Rfree = 0.000) for 4734 atoms. Found 19 (22 requested) and removed 43 (11 requested) atoms. Cycle 3: After refmac, R = 0.2290 (Rfree = 0.000) for 4681 atoms. Found 11 (22 requested) and removed 44 (11 requested) atoms. Cycle 4: After refmac, R = 0.2266 (Rfree = 0.000) for 4625 atoms. Found 17 (22 requested) and removed 41 (11 requested) atoms. Cycle 5: After refmac, R = 0.2212 (Rfree = 0.000) for 4580 atoms. Found 17 (21 requested) and removed 26 (10 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.47 3.42 Search for helices and strands: 0 residues in 0 chains, 4672 seeds are put forward NCS extension: 29 residues added (5 deleted due to clashes), 4701 seeds are put forward Round 1: 303 peptides, 50 chains. Longest chain 15 peptides. Score 0.418 Round 2: 361 peptides, 53 chains. Longest chain 16 peptides. Score 0.508 Round 3: 362 peptides, 48 chains. Longest chain 20 peptides. Score 0.551 Round 4: 369 peptides, 50 chains. Longest chain 20 peptides. Score 0.548 Round 5: 374 peptides, 45 chains. Longest chain 21 peptides. Score 0.595 Taking the results from Round 5 Chains 50, Residues 329, Estimated correctness of the model 0.0 % 3 chains (31 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 10682 restraints for refining 4840 atoms. 9304 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2140 (Rfree = 0.000) for 4840 atoms. Found 18 (23 requested) and removed 41 (11 requested) atoms. Cycle 7: After refmac, R = 0.2075 (Rfree = 0.000) for 4770 atoms. Found 21 (22 requested) and removed 44 (11 requested) atoms. Cycle 8: After refmac, R = 0.1899 (Rfree = 0.000) for 4733 atoms. Found 14 (22 requested) and removed 27 (11 requested) atoms. Cycle 9: After refmac, R = 0.1911 (Rfree = 0.000) for 4706 atoms. Found 21 (22 requested) and removed 28 (11 requested) atoms. Cycle 10: After refmac, R = 0.1811 (Rfree = 0.000) for 4687 atoms. Found 12 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.49 3.44 Search for helices and strands: 0 residues in 0 chains, 4777 seeds are put forward NCS extension: 25 residues added (3 deleted due to clashes), 4802 seeds are put forward Round 1: 311 peptides, 58 chains. Longest chain 13 peptides. Score 0.360 Round 2: 338 peptides, 51 chains. Longest chain 22 peptides. Score 0.481 Round 3: 333 peptides, 46 chains. Longest chain 16 peptides. Score 0.514 Round 4: 332 peptides, 41 chains. Longest chain 23 peptides. Score 0.554 Round 5: 337 peptides, 46 chains. Longest chain 19 peptides. Score 0.522 Taking the results from Round 4 Chains 42, Residues 291, Estimated correctness of the model 0.0 % 4 chains (43 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 10938 restraints for refining 4837 atoms. 9670 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2200 (Rfree = 0.000) for 4837 atoms. Found 13 (23 requested) and removed 41 (11 requested) atoms. Cycle 12: After refmac, R = 0.1971 (Rfree = 0.000) for 4773 atoms. Found 17 (22 requested) and removed 29 (11 requested) atoms. Cycle 13: After refmac, R = 0.1826 (Rfree = 0.000) for 4751 atoms. Found 17 (22 requested) and removed 31 (11 requested) atoms. Cycle 14: After refmac, R = 0.1549 (Rfree = 0.000) for 4720 atoms. Found 5 (22 requested) and removed 22 (11 requested) atoms. Cycle 15: After refmac, R = 0.1679 (Rfree = 0.000) for 4694 atoms. Found 15 (22 requested) and removed 19 (11 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.53 3.48 Search for helices and strands: 0 residues in 0 chains, 4786 seeds are put forward NCS extension: 33 residues added (0 deleted due to clashes), 4819 seeds are put forward Round 1: 293 peptides, 52 chains. Longest chain 11 peptides. Score 0.377 Round 2: 318 peptides, 49 chains. Longest chain 17 peptides. Score 0.459 Round 3: 318 peptides, 48 chains. Longest chain 18 peptides. Score 0.467 Round 4: 328 peptides, 52 chains. Longest chain 13 peptides. Score 0.452 Round 5: 339 peptides, 47 chains. Longest chain 20 peptides. Score 0.517 Taking the results from Round 5 Chains 48, Residues 292, Estimated correctness of the model 0.0 % 5 chains (33 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11031 restraints for refining 4840 atoms. 9820 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2229 (Rfree = 0.000) for 4840 atoms. Found 17 (23 requested) and removed 40 (11 requested) atoms. Cycle 17: After refmac, R = 0.2075 (Rfree = 0.000) for 4784 atoms. Found 22 (22 requested) and removed 31 (11 requested) atoms. Cycle 18: After refmac, R = 0.1980 (Rfree = 0.000) for 4748 atoms. Found 20 (22 requested) and removed 35 (11 requested) atoms. Cycle 19: After refmac, R = 0.1854 (Rfree = 0.000) for 4717 atoms. Found 20 (22 requested) and removed 27 (11 requested) atoms. Cycle 20: After refmac, R = 0.1851 (Rfree = 0.000) for 4706 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.48 3.43 Search for helices and strands: 0 residues in 0 chains, 4818 seeds are put forward NCS extension: 19 residues added (1 deleted due to clashes), 4837 seeds are put forward Round 1: 289 peptides, 53 chains. Longest chain 14 peptides. Score 0.358 Round 2: 329 peptides, 49 chains. Longest chain 22 peptides. Score 0.481 Round 3: 315 peptides, 46 chains. Longest chain 16 peptides. Score 0.479 Round 4: 316 peptides, 46 chains. Longest chain 18 peptides. Score 0.481 Round 5: 316 peptides, 47 chains. Longest chain 22 peptides. Score 0.472 Taking the results from Round 4 Chains 50, Residues 270, Estimated correctness of the model 0.0 % 5 chains (41 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 10858 restraints for refining 4841 atoms. 9681 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2177 (Rfree = 0.000) for 4841 atoms. Found 16 (23 requested) and removed 38 (11 requested) atoms. Cycle 22: After refmac, R = 0.2188 (Rfree = 0.000) for 4797 atoms. Found 22 (22 requested) and removed 30 (11 requested) atoms. Cycle 23: After refmac, R = 0.2024 (Rfree = 0.000) for 4784 atoms. Found 22 (22 requested) and removed 34 (11 requested) atoms. Cycle 24: After refmac, R = 0.1990 (Rfree = 0.000) for 4763 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. Cycle 25: After refmac, R = 0.1909 (Rfree = 0.000) for 4748 atoms. Found 22 (22 requested) and removed 28 (11 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.52 3.47 Search for helices and strands: 0 residues in 0 chains, 4845 seeds are put forward NCS extension: 26 residues added (0 deleted due to clashes), 4871 seeds are put forward Round 1: 266 peptides, 50 chains. Longest chain 15 peptides. Score 0.335 Round 2: 291 peptides, 47 chains. Longest chain 16 peptides. Score 0.420 Round 3: 301 peptides, 45 chains. Longest chain 17 peptides. Score 0.460 Round 4: 313 peptides, 46 chains. Longest chain 18 peptides. Score 0.475 Round 5: 316 peptides, 45 chains. Longest chain 19 peptides. Score 0.490 Taking the results from Round 5 Chains 45, Residues 271, Estimated correctness of the model 0.0 % 3 chains (18 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11184 restraints for refining 4840 atoms. 10099 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2233 (Rfree = 0.000) for 4840 atoms. Found 23 (23 requested) and removed 28 (11 requested) atoms. Cycle 27: After refmac, R = 0.2115 (Rfree = 0.000) for 4791 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 28: After refmac, R = 0.2030 (Rfree = 0.000) for 4762 atoms. Found 20 (22 requested) and removed 27 (11 requested) atoms. Cycle 29: After refmac, R = 0.1600 (Rfree = 0.000) for 4743 atoms. Found 7 (22 requested) and removed 17 (11 requested) atoms. Cycle 30: After refmac, R = 0.1636 (Rfree = 0.000) for 4729 atoms. Found 5 (22 requested) and removed 22 (11 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.51 3.46 Search for helices and strands: 0 residues in 0 chains, 4799 seeds are put forward NCS extension: 29 residues added (1 deleted due to clashes), 4828 seeds are put forward Round 1: 271 peptides, 52 chains. Longest chain 16 peptides. Score 0.327 Round 2: 299 peptides, 51 chains. Longest chain 17 peptides. Score 0.400 Round 3: 320 peptides, 50 chains. Longest chain 18 peptides. Score 0.454 Round 4: 314 peptides, 49 chains. Longest chain 18 peptides. Score 0.450 Round 5: 313 peptides, 45 chains. Longest chain 18 peptides. Score 0.484 Taking the results from Round 5 Chains 45, Residues 268, Estimated correctness of the model 0.0 % 1 chains (6 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11471 restraints for refining 4839 atoms. 10423 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2264 (Rfree = 0.000) for 4839 atoms. Found 22 (23 requested) and removed 28 (11 requested) atoms. Cycle 32: After refmac, R = 0.2169 (Rfree = 0.000) for 4811 atoms. Found 22 (22 requested) and removed 37 (11 requested) atoms. Cycle 33: After refmac, R = 0.1652 (Rfree = 0.000) for 4787 atoms. Found 3 (22 requested) and removed 22 (11 requested) atoms. Cycle 34: After refmac, R = 0.1561 (Rfree = 0.000) for 4756 atoms. Found 2 (22 requested) and removed 18 (11 requested) atoms. Cycle 35: After refmac, R = 0.1532 (Rfree = 0.000) for 4738 atoms. Found 5 (22 requested) and removed 15 (11 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.52 3.47 Search for helices and strands: 0 residues in 0 chains, 4809 seeds are put forward NCS extension: 26 residues added (6 deleted due to clashes), 4835 seeds are put forward Round 1: 260 peptides, 52 chains. Longest chain 13 peptides. Score 0.300 Round 2: 291 peptides, 52 chains. Longest chain 17 peptides. Score 0.373 Round 3: 295 peptides, 45 chains. Longest chain 20 peptides. Score 0.447 Round 4: 301 peptides, 49 chains. Longest chain 13 peptides. Score 0.423 Round 5: 330 peptides, 51 chains. Longest chain 18 peptides. Score 0.465 Taking the results from Round 5 Chains 53, Residues 279, Estimated correctness of the model 0.0 % 5 chains (29 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11102 restraints for refining 4840 atoms. 9960 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2161 (Rfree = 0.000) for 4840 atoms. Found 23 (23 requested) and removed 26 (11 requested) atoms. Cycle 37: After refmac, R = 0.2130 (Rfree = 0.000) for 4807 atoms. Found 22 (22 requested) and removed 25 (11 requested) atoms. Cycle 38: After refmac, R = 0.1914 (Rfree = 0.000) for 4791 atoms. Found 22 (22 requested) and removed 29 (11 requested) atoms. Cycle 39: After refmac, R = 0.1911 (Rfree = 0.000) for 4770 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 40: After refmac, R = 0.1528 (Rfree = 0.000) for 4763 atoms. Found 3 (22 requested) and removed 17 (11 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.53 3.48 Search for helices and strands: 0 residues in 0 chains, 4860 seeds are put forward NCS extension: 14 residues added (0 deleted due to clashes), 4874 seeds are put forward Round 1: 249 peptides, 51 chains. Longest chain 13 peptides. Score 0.284 Round 2: 264 peptides, 44 chains. Longest chain 11 peptides. Score 0.390 Round 3: 269 peptides, 46 chains. Longest chain 10 peptides. Score 0.381 Round 4: 291 peptides, 45 chains. Longest chain 14 peptides. Score 0.439 Round 5: 290 peptides, 48 chains. Longest chain 13 peptides. Score 0.409 Taking the results from Round 4 Chains 45, Residues 246, Estimated correctness of the model 0.0 % 3 chains (17 residues) have been docked in sequence ------------------------------------------------------ 6601 reflections ( 99.58 % complete ) and 11298 restraints for refining 4838 atoms. 10301 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2154 (Rfree = 0.000) for 4838 atoms. Found 21 (23 requested) and removed 38 (11 requested) atoms. Cycle 42: After refmac, R = 0.1970 (Rfree = 0.000) for 4803 atoms. Found 22 (22 requested) and removed 22 (11 requested) atoms. Cycle 43: After refmac, R = 0.1956 (Rfree = 0.000) for 4788 atoms. Found 22 (22 requested) and removed 23 (11 requested) atoms. Failed to save intermediate PDB Cycle 44: After refmac, R = 0.1861 (Rfree = 0.000) for 4778 atoms. Found 22 (22 requested) and removed 26 (11 requested) atoms. Cycle 45: After refmac, R = 0.1424 (Rfree = 0.000) for 4765 atoms. Found 9 (22 requested) and removed 16 (11 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.51 3.46 Search for helices and strands: 0 residues in 0 chains, 4828 seeds are put forward NCS extension: 15 residues added (0 deleted due to clashes), 4843 seeds are put forward Round 1: 228 peptides, 43 chains. Longest chain 9 peptides. Score 0.316 Round 2: 243 peptides, 41 chains. Longest chain 11 peptides. Score 0.372 Round 3: 244 peptides, 36 chains. Longest chain 16 peptides. Score 0.424 Round 4: 253 peptides, 36 chains. Longest chain 18 peptides. Score 0.444 Round 5: 244 peptides, 36 chains. Longest chain 16 peptides. Score 0.424 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 40, Residues 217, Estimated correctness of the model 0.0 % 5 chains (45 residues) have been docked in sequence Sequence coverage is 20 % Consider running further cycles of model building using 2ich-4_warpNtrace.pdb as input Building loops using Loopy2018 40 chains (217 residues) following loop building 5 chains (45 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 6601 reflections ( 99.58 % complete ) and 11244 restraints for refining 4840 atoms. 10259 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2224 (Rfree = 0.000) for 4840 atoms. Found 0 (23 requested) and removed 11 (11 requested) atoms. Cycle 47: After refmac, R = 0.2145 (Rfree = 0.000) for 4814 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 48: After refmac, R = 0.2080 (Rfree = 0.000) for 4789 atoms. Found 0 (22 requested) and removed 11 (11 requested) atoms. Cycle 49: After refmac, R = 0.1959 (Rfree = 0.000) for 4774 atoms. TimeTaking 52.82