null Tue 25 Dec 19:27:55 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 2ghr-4.0-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-4.0-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2ghr-4.0-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-4.0-parrot-hancs 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/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-4.0-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-4.0-parrot-hancs ############### 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 ============================================================ Tue 25 Dec 19:28:05 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/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-4.0-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2ghr-4.0-parrot-hancs/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 222 and 0 Target number of residues in the AU: 222 Target solvent content: 0.6527 Checking the provided sequence file Detected sequence length: 302 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 302 Adjusted target solvent content: 0.53 Input MTZ file: 2ghr-4.0-parrot-hancs.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: 91 Cell parameters: 95.828 95.828 75.339 90.000 90.000 90.000 Input sequence file: 2ghr-4.0-parrot-hancs.fasta_lf Building free atoms model in initial map for 2416 target number of atoms Had to go as low as 0.65 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 Loops will be built when appropriate and at the last cycle Resolution range: 95.828 4.000 Wilson plot Bfac: 79.70 3237 reflections ( 99.57 % complete ) and 0 restraints for refining 2662 atoms. Observations/parameters ratio is 0.30 ------------------------------------------------------ Starting model: R = 0.3400 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.3531 (Rfree = 0.000) for 2662 atoms. Found 12 (12 requested) and removed 59 (6 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.59 3.45 Search for helices and strands: 0 residues in 0 chains, 2628 seeds are put forward Round 1: 93 peptides, 19 chains. Longest chain 8 peptides. Score 0.267 Round 2: 137 peptides, 23 chains. Longest chain 9 peptides. Score 0.403 Round 3: 138 peptides, 21 chains. Longest chain 11 peptides. Score 0.448 Round 4: 138 peptides, 20 chains. Longest chain 16 peptides. Score 0.467 Round 5: 136 peptides, 22 chains. Longest chain 12 peptides. Score 0.419 Taking the results from Round 4 Chains 20, Residues 118, Estimated correctness of the model 0.0 % 1 chains (13 residues) have been docked in sequence ------------------------------------------------------ 3237 reflections ( 99.57 % complete ) and 4646 restraints for refining 2068 atoms. 4123 conditional restraints added. Observations/parameters ratio is 0.39 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3148 (Rfree = 0.000) for 2068 atoms. Found 9 (9 requested) and removed 34 (4 requested) atoms. Cycle 2: After refmac, R = 0.2987 (Rfree = 0.000) for 1988 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 3: After refmac, R = 0.2856 (Rfree = 0.000) for 1958 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 4: After refmac, R = 0.2826 (Rfree = 0.000) for 1938 atoms. Found 9 (9 requested) and removed 5 (4 requested) atoms. Cycle 5: After refmac, R = 0.2357 (Rfree = 0.000) for 1924 atoms. Found 3 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 1973 seeds are put forward Round 1: 127 peptides, 21 chains. Longest chain 14 peptides. Score 0.397 Round 2: 145 peptides, 24 chains. Longest chain 13 peptides. Score 0.420 Round 3: 154 peptides, 26 chains. Longest chain 12 peptides. Score 0.421 Round 4: 154 peptides, 24 chains. Longest chain 13 peptides. Score 0.460 Round 5: 150 peptides, 25 chains. Longest chain 12 peptides. Score 0.423 Taking the results from Round 4 Chains 24, Residues 130, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3237 reflections ( 99.57 % complete ) and 4365 restraints for refining 1929 atoms. 3869 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2687 (Rfree = 0.000) for 1929 atoms. Found 5 (9 requested) and removed 15 (4 requested) atoms. Cycle 7: After refmac, R = 0.2710 (Rfree = 0.000) for 1884 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. Cycle 8: After refmac, R = 0.2591 (Rfree = 0.000) for 1856 atoms. Found 6 (8 requested) and removed 7 (4 requested) atoms. Cycle 9: After refmac, R = 0.2358 (Rfree = 0.000) for 1839 atoms. Found 8 (8 requested) and removed 6 (4 requested) atoms. Cycle 10: After refmac, R = 0.1980 (Rfree = 0.000) for 1834 atoms. Found 2 (8 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.65 3.51 Search for helices and strands: 0 residues in 0 chains, 1912 seeds are put forward Round 1: 142 peptides, 24 chains. Longest chain 14 peptides. Score 0.406 Round 2: 150 peptides, 24 chains. Longest chain 11 peptides. Score 0.442 Round 3: 155 peptides, 24 chains. Longest chain 12 peptides. Score 0.464 Round 4: 157 peptides, 19 chains. Longest chain 30 peptides. Score 0.562 Round 5: 149 peptides, 20 chains. Longest chain 20 peptides. Score 0.513 Taking the results from Round 4 Chains 19, Residues 138, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3237 reflections ( 99.57 % complete ) and 4618 restraints for refining 2033 atoms. 4085 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2652 (Rfree = 0.000) for 2033 atoms. Found 9 (9 requested) and removed 121 (4 requested) atoms. Cycle 12: After refmac, R = 0.2412 (Rfree = 0.000) for 1900 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 13: After refmac, R = 0.2503 (Rfree = 0.000) for 1886 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 14: After refmac, R = 0.2370 (Rfree = 0.000) for 1876 atoms. Found 4 (8 requested) and removed 6 (4 requested) atoms. Cycle 15: After refmac, R = 0.2539 (Rfree = 0.000) for 1865 atoms. Found 8 (8 requested) and removed 4 (4 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.69 3.55 Search for helices and strands: 0 residues in 0 chains, 1959 seeds are put forward Round 1: 132 peptides, 25 chains. Longest chain 8 peptides. Score 0.338 Round 2: 144 peptides, 23 chains. Longest chain 12 peptides. Score 0.435 Round 3: 147 peptides, 24 chains. Longest chain 11 peptides. Score 0.429 Round 4: 141 peptides, 23 chains. Longest chain 11 peptides. Score 0.421 Round 5: 159 peptides, 27 chains. Longest chain 12 peptides. Score 0.425 Taking the results from Round 2 Chains 23, Residues 121, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3237 reflections ( 99.57 % complete ) and 4422 restraints for refining 1947 atoms. 3961 conditional restraints added. Observations/parameters ratio is 0.42 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2611 (Rfree = 0.000) for 1947 atoms. Found 9 (9 requested) and removed 30 (4 requested) atoms. Cycle 17: After refmac, R = 0.2437 (Rfree = 0.000) for 1912 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 18: After refmac, R = 0.2555 (Rfree = 0.000) for 1891 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 19: After refmac, R = 0.2422 (Rfree = 0.000) for 1871 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. Cycle 20: After refmac, R = 0.2503 (Rfree = 0.000) for 1861 atoms. Found 8 (8 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 1938 seeds are put forward Round 1: 135 peptides, 28 chains. Longest chain 10 peptides. Score 0.290 Round 2: 160 peptides, 27 chains. Longest chain 13 peptides. Score 0.429 Round 3: 146 peptides, 23 chains. Longest chain 13 peptides. Score 0.444 Round 4: 157 peptides, 23 chains. Longest chain 16 peptides. Score 0.491 Round 5: 149 peptides, 24 chains. Longest chain 14 peptides. Score 0.438 Taking the results from Round 4 Chains 23, Residues 134, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3237 reflections ( 99.57 % complete ) and 4463 restraints for refining 2007 atoms. 3950 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2683 (Rfree = 0.000) for 2007 atoms. Found 9 (9 requested) and removed 36 (4 requested) atoms. Cycle 22: After refmac, R = 0.2549 (Rfree = 0.000) for 1950 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 23: After refmac, R = 0.2387 (Rfree = 0.000) for 1928 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 24: After refmac, R = 0.2348 (Rfree = 0.000) for 1922 atoms. Found 7 (9 requested) and removed 10 (4 requested) atoms. Cycle 25: After refmac, R = 0.2385 (Rfree = 0.000) for 1907 atoms. Found 9 (9 requested) and removed 9 (4 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.63 3.49 Search for helices and strands: 0 residues in 0 chains, 1995 seeds are put forward Round 1: 137 peptides, 27 chains. Longest chain 12 peptides. Score 0.321 Round 2: 140 peptides, 23 chains. Longest chain 11 peptides. Score 0.417 Round 3: 154 peptides, 26 chains. Longest chain 12 peptides. Score 0.421 Round 4: 154 peptides, 25 chains. Longest chain 18 peptides. Score 0.441 Round 5: 146 peptides, 25 chains. Longest chain 13 peptides. Score 0.405 Taking the results from Round 4 Chains 25, Residues 129, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3237 reflections ( 99.57 % complete ) and 4722 restraints for refining 2048 atoms. 4231 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2668 (Rfree = 0.000) for 2048 atoms. Found 9 (9 requested) and removed 16 (4 requested) atoms. Cycle 27: After refmac, R = 0.2454 (Rfree = 0.000) for 2009 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 28: After refmac, R = 0.2417 (Rfree = 0.000) for 1992 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 29: After refmac, R = 0.2407 (Rfree = 0.000) for 1982 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 30: After refmac, R = 0.2443 (Rfree = 0.000) for 1972 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.62 3.48 Search for helices and strands: 0 residues in 0 chains, 2059 seeds are put forward Round 1: 103 peptides, 22 chains. Longest chain 7 peptides. Score 0.253 Round 2: 124 peptides, 22 chains. Longest chain 10 peptides. Score 0.362 Round 3: 118 peptides, 20 chains. Longest chain 13 peptides. Score 0.375 Round 4: 128 peptides, 23 chains. Longest chain 8 peptides. Score 0.360 Round 5: 139 peptides, 22 chains. Longest chain 14 peptides. Score 0.432 Taking the results from Round 5 Chains 22, Residues 117, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3237 reflections ( 99.57 % complete ) and 4958 restraints for refining 2126 atoms. 4512 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2682 (Rfree = 0.000) for 2126 atoms. Found 10 (10 requested) and removed 12 (5 requested) atoms. Cycle 32: After refmac, R = 0.2584 (Rfree = 0.000) for 2101 atoms. Found 10 (10 requested) and removed 11 (5 requested) atoms. Cycle 33: After refmac, R = 0.2708 (Rfree = 0.000) for 2078 atoms. Found 9 (9 requested) and removed 12 (4 requested) atoms. Cycle 34: After refmac, R = 0.2357 (Rfree = 0.000) for 2066 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. Cycle 35: After refmac, R = 0.2380 (Rfree = 0.000) for 2048 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.60 3.46 Search for helices and strands: 0 residues in 0 chains, 2122 seeds are put forward Round 1: 96 peptides, 18 chains. Longest chain 8 peptides. Score 0.307 Round 2: 116 peptides, 21 chains. Longest chain 15 peptides. Score 0.343 Round 3: 127 peptides, 20 chains. Longest chain 15 peptides. Score 0.418 Round 4: 137 peptides, 21 chains. Longest chain 14 peptides. Score 0.443 Round 5: 133 peptides, 20 chains. Longest chain 13 peptides. Score 0.445 Taking the results from Round 5 Chains 20, Residues 113, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3237 reflections ( 99.57 % complete ) and 4953 restraints for refining 2123 atoms. 4521 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 36: After refmac, R = 0.3446 (Rfree = 0.000) for 2123 atoms. Found 10 (10 requested) and removed 30 (5 requested) atoms. Cycle 37: After refmac, R = 0.3265 (Rfree = 0.000) for 2078 atoms. Found 9 (9 requested) and removed 19 (4 requested) atoms. Cycle 38: After refmac, R = 0.2850 (Rfree = 0.000) for 2040 atoms. Found 9 (9 requested) and removed 10 (4 requested) atoms. Cycle 39: After refmac, R = 0.2750 (Rfree = 0.000) for 2023 atoms. Found 3 (9 requested) and removed 11 (4 requested) atoms. Cycle 40: After refmac, R = 0.2436 (Rfree = 0.000) for 2006 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.63 3.49 Search for helices and strands: 0 residues in 0 chains, 2072 seeds are put forward Round 1: 92 peptides, 18 chains. Longest chain 9 peptides. Score 0.285 Round 2: 112 peptides, 20 chains. Longest chain 11 peptides. Score 0.345 Round 3: 120 peptides, 20 chains. Longest chain 10 peptides. Score 0.385 Round 4: 106 peptides, 18 chains. Longest chain 11 peptides. Score 0.359 Round 5: 119 peptides, 18 chains. Longest chain 12 peptides. Score 0.422 Taking the results from Round 5 Chains 18, Residues 101, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence ------------------------------------------------------ 3237 reflections ( 99.57 % complete ) and 5050 restraints for refining 2138 atoms. 4664 conditional restraints added. Observations/parameters ratio is 0.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2999 (Rfree = 0.000) for 2138 atoms. Found 10 (10 requested) and removed 24 (5 requested) atoms. Cycle 42: After refmac, R = 0.2601 (Rfree = 0.000) for 2099 atoms. Found 10 (10 requested) and removed 14 (5 requested) atoms. Cycle 43: After refmac, R = 0.2554 (Rfree = 0.000) for 2082 atoms. Found 9 (9 requested) and removed 6 (4 requested) atoms. Cycle 44: After refmac, R = 0.2307 (Rfree = 0.000) for 2070 atoms. Found 9 (9 requested) and removed 7 (4 requested) atoms. Cycle 45: After refmac, R = 0.2610 (Rfree = 0.000) for 2058 atoms. Found 9 (9 requested) and removed 8 (4 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.67 3.53 Search for helices and strands: 0 residues in 0 chains, 2120 seeds are put forward Round 1: 78 peptides, 17 chains. Longest chain 7 peptides. Score 0.229 Round 2: 97 peptides, 20 chains. Longest chain 8 peptides. Score 0.266 Round 3: 100 peptides, 19 chains. Longest chain 9 peptides. Score 0.305 Round 4: 108 peptides, 20 chains. Longest chain 10 peptides. Score 0.325 Round 5: 110 peptides, 19 chains. Longest chain 14 peptides. Score 0.357 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 19, Residues 91, Estimated correctness of the model 0.0 % 0 chains (0 residues) have been docked in sequence Sequence coverage is 0 % Consider running further cycles of model building using 2ghr-4_warpNtrace.pdb as input ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 3237 reflections ( 99.57 % complete ) and 4686 restraints for refining 2002 atoms. 4341 conditional restraints added. Observations/parameters ratio is 0.40 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3186 (Rfree = 0.000) for 2002 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 47: After refmac, R = 0.2874 (Rfree = 0.000) for 1973 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 48: After refmac, R = 0.2891 (Rfree = 0.000) for 1953 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Cycle 49: After refmac, R = 0.2599 (Rfree = 0.000) for 1937 atoms. Found 0 (9 requested) and removed 4 (4 requested) atoms. Writing output files ... Normal termination of warpNtrace Tue 25 Dec 20:11:36 GMT 2018 Job finished. TimeTaking 43.68 Used memory is bytes: 19149552