Mon 24 Dec 01:06:31 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2hq7-2.0-parrot-mrncs X-ray data file /users/emra500/scratch/Dataset/mrncsChltofom/2hq7-2.0-parrot-mrncs.mtz Sequence file /users/emra500/scratch/Dataset/mrncsChltofom/2hq7-2.0-parrot-mrncs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-parrot-mrncs 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/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-parrot-mrncs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-parrot-mrncs ############### 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 01:06:41 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/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-parrot-mrncs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/mrncs/ArpWArp/wArpResults/WorkingDir/2hq7-2.0-parrot-mrncs/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 257 and 0 Target number of residues in the AU: 257 Target solvent content: 0.5089 Checking the provided sequence file Detected sequence length: 146 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 292 Adjusted target solvent content: 0.44 Input MTZ file: 2hq7-2.0-parrot-mrncs.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: 5 Cell parameters: 85.850 36.790 97.970 90.000 113.753 90.000 Input sequence file: 2hq7-2.0-parrot-mrncs.fasta_lf Building free atoms model in initial map for 2336 target number of atoms Had to go as low as 0.50 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: 89.671 2.000 Wilson plot Bfac: 25.26 19227 reflections ( 99.63 % complete ) and 0 restraints for refining 2616 atoms. Observations/parameters ratio is 1.84 ------------------------------------------------------ Starting model: R = 0.3114 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2630 (Rfree = 0.000) for 2616 atoms. Found 48 (89 requested) and removed 49 (44 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 2.13 2.31 NCS extension: 0 residues added, 2615 seeds are put forward Round 1: 208 peptides, 21 chains. Longest chain 16 peptides. Score 0.757 Round 2: 230 peptides, 15 chains. Longest chain 33 peptides. Score 0.863 Round 3: 250 peptides, 10 chains. Longest chain 56 peptides. Score 0.921 Round 4: 251 peptides, 8 chains. Longest chain 63 peptides. Score 0.933 Round 5: 254 peptides, 6 chains. Longest chain 91 peptides. Score 0.945 Taking the results from Round 5 Chains 6, Residues 248, Estimated correctness of the model 99.6 % 5 chains (243 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 98 A and 103 A Built loop between residues 43 B and 46 B Built loop between residues 73 B and 80 B 3 chains (260 residues) following loop building 2 chains (255 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2456 restraints for refining 2378 atoms. 325 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2896 (Rfree = 0.000) for 2378 atoms. Found 46 (81 requested) and removed 44 (40 requested) atoms. Cycle 2: After refmac, R = 0.2613 (Rfree = 0.000) for 2377 atoms. Found 36 (79 requested) and removed 41 (40 requested) atoms. Cycle 3: After refmac, R = 0.2431 (Rfree = 0.000) for 2360 atoms. Found 37 (78 requested) and removed 37 (40 requested) atoms. Cycle 4: After refmac, R = 0.2317 (Rfree = 0.000) for 2356 atoms. Found 28 (75 requested) and removed 20 (40 requested) atoms. Cycle 5: After refmac, R = 0.2246 (Rfree = 0.000) for 2361 atoms. Found 35 (74 requested) and removed 17 (40 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 2.08 2.25 NCS extension: 3 residues added (6 deleted due to clashes), 2382 seeds are put forward Round 1: 263 peptides, 4 chains. Longest chain 122 peptides. Score 0.959 Round 2: 261 peptides, 6 chains. Longest chain 78 peptides. Score 0.949 Round 3: 264 peptides, 6 chains. Longest chain 87 peptides. Score 0.951 Round 4: 265 peptides, 6 chains. Longest chain 79 peptides. Score 0.952 Round 5: 260 peptides, 7 chains. Longest chain 86 peptides. Score 0.944 Taking the results from Round 1 Chains 4, Residues 259, Estimated correctness of the model 99.8 % 3 chains (252 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 B and 103 B 3 chains (261 residues) following loop building 2 chains (254 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2435 restraints for refining 2378 atoms. 309 conditional restraints added. Observations/parameters ratio is 2.02 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2378 (Rfree = 0.000) for 2378 atoms. Found 58 (75 requested) and removed 41 (40 requested) atoms. Cycle 7: After refmac, R = 0.2256 (Rfree = 0.000) for 2391 atoms. Found 40 (74 requested) and removed 41 (41 requested) atoms. Cycle 8: After refmac, R = 0.2164 (Rfree = 0.000) for 2389 atoms. Found 35 (71 requested) and removed 19 (40 requested) atoms. Cycle 9: After refmac, R = 0.2107 (Rfree = 0.000) for 2400 atoms. Found 36 (71 requested) and removed 18 (41 requested) atoms. Cycle 10: After refmac, R = 0.2060 (Rfree = 0.000) for 2416 atoms. Found 27 (71 requested) and removed 18 (41 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 2.10 2.28 NCS extension: 3 residues added (8 deleted due to clashes), 2428 seeds are put forward Round 1: 264 peptides, 4 chains. Longest chain 124 peptides. Score 0.960 Round 2: 266 peptides, 4 chains. Longest chain 124 peptides. Score 0.961 Round 3: 261 peptides, 6 chains. Longest chain 78 peptides. Score 0.949 Round 4: 260 peptides, 6 chains. Longest chain 86 peptides. Score 0.949 Round 5: 262 peptides, 6 chains. Longest chain 97 peptides. Score 0.950 Taking the results from Round 2 Chains 4, Residues 262, Estimated correctness of the model 99.8 % 3 chains (255 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 104 A 3 chains (264 residues) following loop building 2 chains (257 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2459 restraints for refining 2418 atoms. 303 conditional restraints added. Observations/parameters ratio is 1.99 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2273 (Rfree = 0.000) for 2418 atoms. Found 56 (69 requested) and removed 41 (41 requested) atoms. Cycle 12: After refmac, R = 0.2164 (Rfree = 0.000) for 2429 atoms. Found 40 (68 requested) and removed 34 (41 requested) atoms. Cycle 13: After refmac, R = 0.2086 (Rfree = 0.000) for 2432 atoms. Found 41 (66 requested) and removed 21 (41 requested) atoms. Cycle 14: After refmac, R = 0.2034 (Rfree = 0.000) for 2450 atoms. Found 40 (65 requested) and removed 20 (41 requested) atoms. Cycle 15: After refmac, R = 0.1977 (Rfree = 0.000) for 2466 atoms. Found 44 (66 requested) and removed 21 (42 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 2.07 2.24 NCS extension: 3 residues added (6 deleted due to clashes), 2492 seeds are put forward Round 1: 263 peptides, 4 chains. Longest chain 94 peptides. Score 0.959 Round 2: 266 peptides, 3 chains. Longest chain 132 peptides. Score 0.965 Round 3: 265 peptides, 4 chains. Longest chain 132 peptides. Score 0.960 Round 4: 263 peptides, 4 chains. Longest chain 97 peptides. Score 0.959 Round 5: 260 peptides, 6 chains. Longest chain 78 peptides. Score 0.949 Taking the results from Round 2 Chains 3, Residues 263, Estimated correctness of the model 99.8 % 3 chains (263 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 100 B and 103 B 2 chains (265 residues) following loop building 2 chains (265 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2420 restraints for refining 2453 atoms. 222 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2210 (Rfree = 0.000) for 2453 atoms. Found 58 (66 requested) and removed 44 (42 requested) atoms. Cycle 17: After refmac, R = 0.2079 (Rfree = 0.000) for 2463 atoms. Found 36 (64 requested) and removed 25 (42 requested) atoms. Cycle 18: After refmac, R = 0.2003 (Rfree = 0.000) for 2474 atoms. Found 42 (62 requested) and removed 24 (42 requested) atoms. Cycle 19: After refmac, R = 0.1962 (Rfree = 0.000) for 2490 atoms. Found 43 (61 requested) and removed 29 (42 requested) atoms. Cycle 20: After refmac, R = 0.1961 (Rfree = 0.000) for 2502 atoms. Found 43 (59 requested) and removed 29 (42 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 2.08 2.25 NCS extension: 0 residues added, 2517 seeds are put forward Round 1: 261 peptides, 4 chains. Longest chain 95 peptides. Score 0.958 Round 2: 261 peptides, 4 chains. Longest chain 95 peptides. Score 0.958 Round 3: 258 peptides, 4 chains. Longest chain 95 peptides. Score 0.957 Round 4: 259 peptides, 7 chains. Longest chain 67 peptides. Score 0.943 Round 5: 258 peptides, 6 chains. Longest chain 95 peptides. Score 0.948 Taking the results from Round 2 Chains 4, Residues 257, Estimated correctness of the model 99.8 % 4 chains (257 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 101 A and 104 A Built loop between residues 73 B and 80 B 2 chains (265 residues) following loop building 2 chains (265 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2400 restraints for refining 2460 atoms. 202 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2214 (Rfree = 0.000) for 2460 atoms. Found 55 (57 requested) and removed 42 (42 requested) atoms. Cycle 22: After refmac, R = 0.2080 (Rfree = 0.000) for 2469 atoms. Found 41 (55 requested) and removed 33 (42 requested) atoms. Cycle 23: After refmac, R = 0.2029 (Rfree = 0.000) for 2474 atoms. Found 47 (54 requested) and removed 33 (42 requested) atoms. Cycle 24: After refmac, R = 0.1979 (Rfree = 0.000) for 2488 atoms. Found 50 (53 requested) and removed 30 (42 requested) atoms. Cycle 25: After refmac, R = 0.1954 (Rfree = 0.000) for 2507 atoms. Found 51 (51 requested) and removed 33 (42 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 2.07 2.24 NCS extension: 0 residues added, 2525 seeds are put forward Round 1: 261 peptides, 3 chains. Longest chain 135 peptides. Score 0.963 Round 2: 261 peptides, 3 chains. Longest chain 135 peptides. Score 0.963 Round 3: 260 peptides, 4 chains. Longest chain 135 peptides. Score 0.958 Round 4: 259 peptides, 6 chains. Longest chain 78 peptides. Score 0.948 Round 5: 259 peptides, 5 chains. Longest chain 95 peptides. Score 0.953 Taking the results from Round 2 Chains 3, Residues 258, Estimated correctness of the model 99.8 % 3 chains (258 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 80 A 2 chains (264 residues) following loop building 2 chains (264 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2419 restraints for refining 2459 atoms. 230 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2180 (Rfree = 0.000) for 2459 atoms. Found 49 (49 requested) and removed 44 (42 requested) atoms. Cycle 27: After refmac, R = 0.2065 (Rfree = 0.000) for 2464 atoms. Found 47 (47 requested) and removed 22 (42 requested) atoms. Cycle 28: After refmac, R = 0.1991 (Rfree = 0.000) for 2488 atoms. Found 41 (48 requested) and removed 25 (42 requested) atoms. Cycle 29: After refmac, R = 0.1948 (Rfree = 0.000) for 2501 atoms. Found 46 (46 requested) and removed 32 (42 requested) atoms. Cycle 30: After refmac, R = 0.1905 (Rfree = 0.000) for 2511 atoms. Found 45 (45 requested) and removed 37 (43 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 2.07 2.24 NCS extension: 0 residues added (3 deleted due to clashes), 2519 seeds are put forward Round 1: 261 peptides, 3 chains. Longest chain 135 peptides. Score 0.963 Round 2: 260 peptides, 4 chains. Longest chain 95 peptides. Score 0.958 Round 3: 256 peptides, 8 chains. Longest chain 64 peptides. Score 0.936 Round 4: 255 peptides, 8 chains. Longest chain 86 peptides. Score 0.936 Round 5: 258 peptides, 7 chains. Longest chain 67 peptides. Score 0.943 Taking the results from Round 1 Chains 3, Residues 258, Estimated correctness of the model 99.8 % 3 chains (258 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 73 A and 80 A 2 chains (264 residues) following loop building 2 chains (264 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2374 restraints for refining 2456 atoms. 185 conditional restraints added. Observations/parameters ratio is 1.96 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2156 (Rfree = 0.000) for 2456 atoms. Found 42 (42 requested) and removed 44 (42 requested) atoms. Cycle 32: After refmac, R = 0.2027 (Rfree = 0.000) for 2453 atoms. Found 42 (42 requested) and removed 20 (42 requested) atoms. Cycle 33: After refmac, R = 0.1958 (Rfree = 0.000) for 2471 atoms. Found 42 (42 requested) and removed 21 (42 requested) atoms. Cycle 34: After refmac, R = 0.1897 (Rfree = 0.000) for 2489 atoms. Found 42 (42 requested) and removed 17 (42 requested) atoms. Cycle 35: After refmac, R = 0.1871 (Rfree = 0.000) for 2510 atoms. Found 43 (43 requested) and removed 23 (43 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 2.07 2.24 NCS extension: 0 residues added (3 deleted due to clashes), 2530 seeds are put forward Round 1: 261 peptides, 4 chains. Longest chain 95 peptides. Score 0.958 Round 2: 263 peptides, 4 chains. Longest chain 98 peptides. Score 0.959 Round 3: 259 peptides, 7 chains. Longest chain 78 peptides. Score 0.943 Round 4: 257 peptides, 9 chains. Longest chain 74 peptides. Score 0.932 Round 5: 260 peptides, 6 chains. Longest chain 98 peptides. Score 0.949 Taking the results from Round 2 Chains 4, Residues 259, Estimated correctness of the model 99.8 % 4 chains (259 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 103 A and 106 A Built loop between residues 75 B and 80 B 2 chains (265 residues) following loop building 2 chains (265 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2379 restraints for refining 2470 atoms. 178 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2153 (Rfree = 0.000) for 2470 atoms. Found 42 (42 requested) and removed 43 (42 requested) atoms. Cycle 37: After refmac, R = 0.2001 (Rfree = 0.000) for 2469 atoms. Found 42 (42 requested) and removed 24 (42 requested) atoms. Cycle 38: After refmac, R = 0.1937 (Rfree = 0.000) for 2485 atoms. Found 42 (42 requested) and removed 22 (42 requested) atoms. Cycle 39: After refmac, R = 0.1885 (Rfree = 0.000) for 2503 atoms. Found 42 (42 requested) and removed 21 (42 requested) atoms. Cycle 40: After refmac, R = 0.1860 (Rfree = 0.000) for 2523 atoms. Found 43 (43 requested) and removed 28 (43 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 2.06 2.23 NCS extension: 3 residues added (1 deleted due to clashes), 2541 seeds are put forward Round 1: 261 peptides, 5 chains. Longest chain 96 peptides. Score 0.954 Round 2: 267 peptides, 2 chains. Longest chain 136 peptides. Score 0.970 Round 3: 262 peptides, 6 chains. Longest chain 67 peptides. Score 0.950 Round 4: 257 peptides, 5 chains. Longest chain 87 peptides. Score 0.952 Round 5: 264 peptides, 5 chains. Longest chain 136 peptides. Score 0.956 Taking the results from Round 2 Chains 2, Residues 265, Estimated correctness of the model 99.9 % 2 chains (265 residues) have been docked in sequence Building loops using Loopy2018 2 chains (265 residues) following loop building 2 chains (265 residues) in sequence following loop building ------------------------------------------------------ 19227 reflections ( 99.63 % complete ) and 2404 restraints for refining 2469 atoms. 203 conditional restraints added. Observations/parameters ratio is 1.95 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2100 (Rfree = 0.000) for 2469 atoms. Found 42 (42 requested) and removed 44 (42 requested) atoms. Cycle 42: After refmac, R = 0.1986 (Rfree = 0.000) for 2465 atoms. Found 42 (42 requested) and removed 24 (42 requested) atoms. Cycle 43: After refmac, R = 0.1930 (Rfree = 0.000) for 2481 atoms. Found 42 (42 requested) and removed 14 (42 requested) atoms. Cycle 44: After refmac, R = 0.1884 (Rfree = 0.000) for 2506 atoms. Found 42 (42 requested) and removed 20 (42 requested) atoms. Cycle 45: After refmac, R = 0.1857 (Rfree = 0.000) for 2526 atoms. Found 43 (43 requested) and removed 31 (43 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 2.07 2.24 NCS extension: 3 residues added (1 deleted due to clashes), 2541 seeds are put forward Round 1: 263 peptides, 4 chains. Longest chain 136 peptides. Score 0.959 Round 2: 258 peptides, 5 chains. Longest chain 123 peptides. Score 0.952 Round 3: 258 peptides, 7 chains. Longest chain 77 peptides. Score 0.943 Round 4: 261 peptides, 5 chains. Longest chain 136 peptides. Score 0.954 Round 5: 256 peptides, 11 chains. Longest chain 66 peptides. Score 0.920 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 259, Estimated correctness of the model 99.8 % 4 chains (258 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 75 B and 79 B Built loop between residues 101 B and 105 B 2 chains (264 residues) following loop building 2 chains (264 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 19227 reflections ( 99.63 % complete ) and 2195 restraints for refining 2148 atoms. Observations/parameters ratio is 2.24 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2544 (Rfree = 0.000) for 2148 atoms. Found 18 (36 requested) and removed 0 (36 requested) atoms. Cycle 47: After refmac, R = 0.2398 (Rfree = 0.000) for 2148 atoms. Found 7 (37 requested) and removed 0 (37 requested) atoms. Cycle 48: After refmac, R = 0.2296 (Rfree = 0.000) for 2148 atoms. Found 4 (37 requested) and removed 0 (37 requested) atoms. Cycle 49: After refmac, R = 0.2236 (Rfree = 0.000) for 2148 atoms. TimeTaking 44.42