null Sun 23 Dec 22:22:59 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 2oc5-1.7-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-1.7-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2oc5-1.7-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-1.7-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/2oc5-1.7-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-1.7-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 ============================================================ Sun 23 Dec 22:23:07 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/2oc5-1.7-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2oc5-1.7-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 351 and 0 Target number of residues in the AU: 351 Target solvent content: 0.4576 Checking the provided sequence file Detected sequence length: 244 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 244 Adjusted target solvent content: 0.62 Input MTZ file: 2oc5-1.7-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: 96 Cell parameters: 77.390 77.390 116.960 90.000 90.000 90.000 Input sequence file: 2oc5-1.7-parrot-hancs.fasta_lf Building free atoms model in initial map for 1952 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 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 Loops will be built when appropriate and at the last cycle Resolution range: 29.240 1.680 Wilson plot Bfac: 15.71 40958 reflections ( 99.39 % complete ) and 0 restraints for refining 2153 atoms. Observations/parameters ratio is 4.76 ------------------------------------------------------ Starting model: R = 0.3184 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2608 (Rfree = 0.000) for 2153 atoms. Found 121 (121 requested) and removed 61 (60 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.82 1.55 Round 1: 194 peptides, 14 chains. Longest chain 40 peptides. Score 0.745 Round 2: 212 peptides, 4 chains. Longest chain 85 peptides. Score 0.877 Round 3: 218 peptides, 2 chains. Longest chain 171 peptides. Score 0.900 Round 4: 218 peptides, 3 chains. Longest chain 116 peptides. Score 0.892 Round 5: 219 peptides, 2 chains. Longest chain 171 peptides. Score 0.901 Taking the results from Round 5 Chains 2, Residues 217, Estimated correctness of the model 99.4 % 2 chains (217 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 191 A and 194 A 1 chains (219 residues) following loop building 1 chains (219 residues) in sequence following loop building ------------------------------------------------------ 40958 reflections ( 99.39 % complete ) and 1987 restraints for refining 2104 atoms. 214 conditional restraints added. Observations/parameters ratio is 4.87 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2540 (Rfree = 0.000) for 2104 atoms. Found 118 (118 requested) and removed 23 (59 requested) atoms. Cycle 2: After refmac, R = 0.2268 (Rfree = 0.000) for 2197 atoms. Found 93 (123 requested) and removed 18 (61 requested) atoms. Cycle 3: After refmac, R = 0.2114 (Rfree = 0.000) for 2266 atoms. Found 84 (127 requested) and removed 24 (63 requested) atoms. Cycle 4: After refmac, R = 0.2055 (Rfree = 0.000) for 2319 atoms. Found 79 (130 requested) and removed 30 (65 requested) atoms. Cycle 5: After refmac, R = 0.2010 (Rfree = 0.000) for 2364 atoms. Found 81 (133 requested) and removed 29 (66 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.75 1.49 Round 1: 220 peptides, 2 chains. Longest chain 157 peptides. Score 0.902 Round 2: 219 peptides, 2 chains. Longest chain 158 peptides. Score 0.901 Round 3: 219 peptides, 2 chains. Longest chain 163 peptides. Score 0.901 Round 4: 218 peptides, 3 chains. Longest chain 113 peptides. Score 0.892 Round 5: 218 peptides, 3 chains. Longest chain 100 peptides. Score 0.892 Taking the results from Round 1 Chains 3, Residues 218, Estimated correctness of the model 99.4 % 2 chains (216 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 175 A and 179 A 1 chains (219 residues) following loop building 1 chains (219 residues) in sequence following loop building ------------------------------------------------------ 40958 reflections ( 99.39 % complete ) and 2079 restraints for refining 2237 atoms. 306 conditional restraints added. Observations/parameters ratio is 4.58 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2088 (Rfree = 0.000) for 2237 atoms. Found 125 (125 requested) and removed 15 (62 requested) atoms. Cycle 7: After refmac, R = 0.2042 (Rfree = 0.000) for 2343 atoms. Found 79 (132 requested) and removed 33 (66 requested) atoms. Cycle 8: After refmac, R = 0.1984 (Rfree = 0.000) for 2384 atoms. Found 71 (134 requested) and removed 33 (67 requested) atoms. Cycle 9: After refmac, R = 0.1957 (Rfree = 0.000) for 2417 atoms. Found 75 (136 requested) and removed 36 (68 requested) atoms. Cycle 10: After refmac, R = 0.1938 (Rfree = 0.000) for 2450 atoms. Found 63 (138 requested) and removed 35 (69 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.75 1.49 Round 1: 220 peptides, 1 chains. Longest chain 220 peptides. Score 0.909 Round 2: 219 peptides, 2 chains. Longest chain 156 peptides. Score 0.901 Round 3: 219 peptides, 2 chains. Longest chain 158 peptides. Score 0.901 Round 4: 220 peptides, 2 chains. Longest chain 157 peptides. Score 0.902 Round 5: 218 peptides, 3 chains. Longest chain 114 peptides. Score 0.892 Taking the results from Round 1 Chains 1, Residues 219, Estimated correctness of the model 99.5 % 1 chains (219 residues) have been docked in sequence ------------------------------------------------------ 40958 reflections ( 99.39 % complete ) and 2136 restraints for refining 2297 atoms. 363 conditional restraints added. Observations/parameters ratio is 4.46 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2021 (Rfree = 0.000) for 2297 atoms. Found 126 (126 requested) and removed 11 (64 requested) atoms. Cycle 12: After refmac, R = 0.1966 (Rfree = 0.000) for 2408 atoms. Found 71 (132 requested) and removed 39 (67 requested) atoms. Cycle 13: After refmac, R = 0.1935 (Rfree = 0.000) for 2437 atoms. Found 72 (132 requested) and removed 35 (68 requested) atoms. Cycle 14: After refmac, R = 0.1922 (Rfree = 0.000) for 2468 atoms. Found 76 (133 requested) and removed 53 (69 requested) atoms. Cycle 15: After refmac, R = 0.1933 (Rfree = 0.000) for 2486 atoms. Found 87 (132 requested) and removed 48 (70 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.75 1.49 Round 1: 220 peptides, 1 chains. Longest chain 220 peptides. Score 0.909 Round 2: 219 peptides, 2 chains. Longest chain 156 peptides. Score 0.901 Round 3: 219 peptides, 2 chains. Longest chain 158 peptides. Score 0.901 Round 4: 219 peptides, 2 chains. Longest chain 163 peptides. Score 0.901 Round 5: 216 peptides, 5 chains. Longest chain 113 peptides. Score 0.874 Taking the results from Round 1 Chains 1, Residues 219, Estimated correctness of the model 99.5 % 1 chains (219 residues) have been docked in sequence ------------------------------------------------------ 40958 reflections ( 99.39 % complete ) and 2192 restraints for refining 2313 atoms. 419 conditional restraints added. Observations/parameters ratio is 4.43 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2028 (Rfree = 0.000) for 2313 atoms. Found 120 (120 requested) and removed 13 (65 requested) atoms. Cycle 17: After refmac, R = 0.1992 (Rfree = 0.000) for 2419 atoms. Found 59 (125 requested) and removed 49 (68 requested) atoms. Cycle 18: After refmac, R = 0.1937 (Rfree = 0.000) for 2425 atoms. Found 73 (122 requested) and removed 28 (68 requested) atoms. Cycle 19: After refmac, R = 0.1913 (Rfree = 0.000) for 2465 atoms. Found 65 (124 requested) and removed 37 (69 requested) atoms. Cycle 20: After refmac, R = 0.1905 (Rfree = 0.000) for 2491 atoms. Found 57 (123 requested) and removed 38 (70 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.75 1.49 Round 1: 220 peptides, 1 chains. Longest chain 220 peptides. Score 0.909 Round 2: 219 peptides, 2 chains. Longest chain 156 peptides. Score 0.901 Round 3: 219 peptides, 2 chains. Longest chain 158 peptides. Score 0.901 Round 4: 217 peptides, 4 chains. Longest chain 65 peptides. Score 0.883 Round 5: 219 peptides, 2 chains. Longest chain 156 peptides. Score 0.901 Taking the results from Round 1 Chains 1, Residues 219, Estimated correctness of the model 99.5 % 1 chains (219 residues) have been docked in sequence ------------------------------------------------------ 40958 reflections ( 99.39 % complete ) and 2191 restraints for refining 2326 atoms. 418 conditional restraints added. Observations/parameters ratio is 4.40 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1998 (Rfree = 0.000) for 2326 atoms. Found 112 (112 requested) and removed 15 (65 requested) atoms. Cycle 22: After refmac, R = 0.1985 (Rfree = 0.000) for 2419 atoms. Found 64 (117 requested) and removed 40 (68 requested) atoms. Cycle 23: After refmac, R = 0.1930 (Rfree = 0.000) for 2440 atoms. Found 75 (115 requested) and removed 22 (68 requested) atoms. Cycle 24: After refmac, R = 0.1903 (Rfree = 0.000) for 2486 atoms. Found 77 (118 requested) and removed 37 (70 requested) atoms. Cycle 25: After refmac, R = 0.1890 (Rfree = 0.000) for 2522 atoms. Found 67 (119 requested) and removed 41 (71 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.75 1.49 Round 1: 220 peptides, 1 chains. Longest chain 220 peptides. Score 0.909 Round 2: 219 peptides, 2 chains. Longest chain 156 peptides. Score 0.901 Round 3: 219 peptides, 2 chains. Longest chain 178 peptides. Score 0.901 Round 4: 219 peptides, 3 chains. Longest chain 100 peptides. Score 0.893 Round 5: 217 peptides, 4 chains. Longest chain 113 peptides. Score 0.883 Taking the results from Round 1 Chains 1, Residues 219, Estimated correctness of the model 99.5 % 1 chains (219 residues) have been docked in sequence ------------------------------------------------------ 40958 reflections ( 99.39 % complete ) and 2201 restraints for refining 2331 atoms. 428 conditional restraints added. Observations/parameters ratio is 4.39 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1999 (Rfree = 0.000) for 2331 atoms. Found 107 (107 requested) and removed 13 (65 requested) atoms. Cycle 27: After refmac, R = 0.1981 (Rfree = 0.000) for 2416 atoms. Found 94 (112 requested) and removed 23 (68 requested) atoms. Cycle 28: After refmac, R = 0.1946 (Rfree = 0.000) for 2482 atoms. Found 77 (114 requested) and removed 39 (69 requested) atoms. Cycle 29: After refmac, R = 0.1913 (Rfree = 0.000) for 2517 atoms. Found 64 (113 requested) and removed 42 (70 requested) atoms. Cycle 30: After refmac, R = 0.1893 (Rfree = 0.000) for 2537 atoms. Found 69 (111 requested) and removed 38 (71 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.75 1.49 Round 1: 219 peptides, 2 chains. Longest chain 158 peptides. Score 0.901 Round 2: 219 peptides, 2 chains. Longest chain 157 peptides. Score 0.901 Round 3: 219 peptides, 2 chains. Longest chain 113 peptides. Score 0.901 Round 4: 219 peptides, 2 chains. Longest chain 178 peptides. Score 0.901 Round 5: 218 peptides, 3 chains. Longest chain 101 peptides. Score 0.892 Taking the results from Round 4 Chains 2, Residues 217, Estimated correctness of the model 99.4 % 2 chains (217 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 198 A and 201 A 1 chains (219 residues) following loop building 1 chains (219 residues) in sequence following loop building ------------------------------------------------------ 40958 reflections ( 99.39 % complete ) and 2192 restraints for refining 2342 atoms. 419 conditional restraints added. Observations/parameters ratio is 4.37 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2003 (Rfree = 0.000) for 2342 atoms. Found 100 (100 requested) and removed 20 (65 requested) atoms. Cycle 32: After refmac, R = 0.1981 (Rfree = 0.000) for 2412 atoms. Found 100 (103 requested) and removed 25 (68 requested) atoms. Cycle 33: After refmac, R = 0.1950 (Rfree = 0.000) for 2484 atoms. Found 64 (106 requested) and removed 45 (69 requested) atoms. Cycle 34: After refmac, R = 0.1891 (Rfree = 0.000) for 2500 atoms. Found 76 (104 requested) and removed 24 (70 requested) atoms. Cycle 35: After refmac, R = 0.1877 (Rfree = 0.000) for 2550 atoms. Found 66 (106 requested) and removed 52 (71 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.74 1.48 Round 1: 219 peptides, 2 chains. Longest chain 156 peptides. Score 0.901 Round 2: 220 peptides, 1 chains. Longest chain 220 peptides. Score 0.909 Round 3: 219 peptides, 2 chains. Longest chain 156 peptides. Score 0.901 Round 4: 218 peptides, 3 chains. Longest chain 113 peptides. Score 0.892 Round 5: 218 peptides, 2 chains. Longest chain 162 peptides. Score 0.900 Taking the results from Round 2 Chains 1, Residues 219, Estimated correctness of the model 99.5 % 1 chains (219 residues) have been docked in sequence ------------------------------------------------------ 40958 reflections ( 99.39 % complete ) and 2262 restraints for refining 2367 atoms. 489 conditional restraints added. Observations/parameters ratio is 4.33 ------------------------------------------------------ Cycle 36: After refmac, R = 0.1983 (Rfree = 0.000) for 2367 atoms. Found 96 (96 requested) and removed 15 (66 requested) atoms. Cycle 37: After refmac, R = 0.1938 (Rfree = 0.000) for 2440 atoms. Found 84 (99 requested) and removed 18 (68 requested) atoms. Cycle 38: After refmac, R = 0.1928 (Rfree = 0.000) for 2500 atoms. Found 61 (102 requested) and removed 52 (70 requested) atoms. Cycle 39: After refmac, R = 0.1901 (Rfree = 0.000) for 2503 atoms. Found 87 (99 requested) and removed 41 (70 requested) atoms. Cycle 40: After refmac, R = 0.1886 (Rfree = 0.000) for 2546 atoms. Found 69 (100 requested) and removed 49 (71 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.74 1.48 Round 1: 220 peptides, 1 chains. Longest chain 220 peptides. Score 0.909 Round 2: 218 peptides, 3 chains. Longest chain 113 peptides. Score 0.892 Round 3: 217 peptides, 3 chains. Longest chain 113 peptides. Score 0.891 Round 4: 218 peptides, 2 chains. Longest chain 156 peptides. Score 0.900 Round 5: 218 peptides, 3 chains. Longest chain 101 peptides. Score 0.892 Taking the results from Round 1 Chains 1, Residues 219, Estimated correctness of the model 99.5 % 1 chains (219 residues) have been docked in sequence ------------------------------------------------------ 40958 reflections ( 99.39 % complete ) and 2190 restraints for refining 2339 atoms. 417 conditional restraints added. Observations/parameters ratio is 4.38 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1986 (Rfree = 0.000) for 2339 atoms. Found 89 (89 requested) and removed 19 (65 requested) atoms. Cycle 42: After refmac, R = 0.1944 (Rfree = 0.000) for 2401 atoms. Found 92 (92 requested) and removed 30 (67 requested) atoms. Cycle 43: After refmac, R = 0.1923 (Rfree = 0.000) for 2459 atoms. Found 70 (94 requested) and removed 42 (69 requested) atoms. Cycle 44: After refmac, R = 0.1902 (Rfree = 0.000) for 2482 atoms. Found 75 (92 requested) and removed 35 (69 requested) atoms. Cycle 45: After refmac, R = 0.1881 (Rfree = 0.000) for 2515 atoms. Found 84 (93 requested) and removed 42 (70 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.74 1.48 Round 1: 219 peptides, 1 chains. Longest chain 219 peptides. Score 0.908 Round 2: 216 peptides, 4 chains. Longest chain 113 peptides. Score 0.882 Round 3: 218 peptides, 2 chains. Longest chain 158 peptides. Score 0.900 Round 4: 217 peptides, 3 chains. Longest chain 106 peptides. Score 0.891 Round 5: 218 peptides, 2 chains. Longest chain 156 peptides. Score 0.900 Taking the results from Round 1 Last building cycle: Chain fragments will be rearranged Chains 1, Residues 218, Estimated correctness of the model 99.5 % 1 chains (218 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 40958 reflections ( 99.39 % complete ) and 1768 restraints for refining 1738 atoms. Observations/parameters ratio is 5.89 ------------------------------------------------------ Cycle 46: After refmac, R = 0.2615 (Rfree = 0.000) for 1738 atoms. Found 64 (64 requested) and removed 0 (64 requested) atoms. Cycle 47: After refmac, R = 0.2407 (Rfree = 0.000) for 1738 atoms. Found 67 (67 requested) and removed 1 (50 requested) atoms. Cycle 48: After refmac, R = 0.2288 (Rfree = 0.000) for 1738 atoms. Found 28 (69 requested) and removed 1 (52 requested) atoms. Cycle 49: After refmac, R = 0.2193 (Rfree = 0.000) for 1738 atoms. Found 20 (70 requested) and removed 3 (53 requested) atoms. Writing output files ... Normal termination of warpNtrace Sun 23 Dec 23:20:28 GMT 2018 Job finished. TimeTaking 57.48 Used memory is bytes: 9740080