Sun 23 Dec 22:22:43 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 2hdo-1.5-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-1.5-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/2hdo-1.5-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-1.5-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/2hdo-1.5-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-1.5-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 22:22:51 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/2hdo-1.5-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/2hdo-1.5-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 225 and 0 Target number of residues in the AU: 225 Target solvent content: 0.4113 Checking the provided sequence file Detected sequence length: 209 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 1 Adjusted target number of residues: 209 Adjusted target solvent content: 0.45 Input MTZ file: 2hdo-1.5-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: 169 Cell parameters: 87.040 87.040 47.290 90.000 90.000 120.000 Input sequence file: 2hdo-1.5-parrot-hancs.fasta_lf Building free atoms model in initial map for 1672 target number of atoms Had to go as low as 0.45 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: 29.474 1.501 Wilson plot Bfac: 9.33 32016 reflections ( 97.74 % complete ) and 0 restraints for refining 1840 atoms. Observations/parameters ratio is 4.35 ------------------------------------------------------ Starting model: R = 0.3368 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2994 (Rfree = 0.000) for 1840 atoms. Found 110 (142 requested) and removed 74 (71 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 1.50 1.60 Round 1: 155 peptides, 16 chains. Longest chain 20 peptides. Score 0.757 Round 2: 181 peptides, 7 chains. Longest chain 58 peptides. Score 0.921 Round 3: 188 peptides, 8 chains. Longest chain 51 peptides. Score 0.922 Round 4: 192 peptides, 5 chains. Longest chain 73 peptides. Score 0.947 Round 5: 201 peptides, 5 chains. Longest chain 70 peptides. Score 0.953 Taking the results from Round 5 Chains 5, Residues 196, Estimated correctness of the model 99.9 % 4 chains (188 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 16 A and 19 A Built loop between residues 137 A and 140 A 3 chains (200 residues) following loop building 2 chains (192 residues) in sequence following loop building ------------------------------------------------------ 32016 reflections ( 97.74 % complete ) and 1891 restraints for refining 1815 atoms. 334 conditional restraints added. Observations/parameters ratio is 4.41 ------------------------------------------------------ Cycle 1: After refmac, R = 0.3108 (Rfree = 0.000) for 1815 atoms. Found 79 (140 requested) and removed 39 (70 requested) atoms. Cycle 2: After refmac, R = 0.2970 (Rfree = 0.000) for 1854 atoms. Found 73 (143 requested) and removed 20 (71 requested) atoms. Cycle 3: After refmac, R = 0.2835 (Rfree = 0.000) for 1906 atoms. Found 72 (148 requested) and removed 6 (74 requested) atoms. Cycle 4: After refmac, R = 0.2775 (Rfree = 0.000) for 1969 atoms. Found 55 (153 requested) and removed 3 (76 requested) atoms. Cycle 5: After refmac, R = 0.2715 (Rfree = 0.000) for 2021 atoms. Found 55 (156 requested) and removed 5 (78 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 1.46 1.56 Round 1: 204 peptides, 2 chains. Longest chain 134 peptides. Score 0.971 Round 2: 204 peptides, 2 chains. Longest chain 135 peptides. Score 0.971 Round 3: 203 peptides, 3 chains. Longest chain 136 peptides. Score 0.966 Round 4: 202 peptides, 3 chains. Longest chain 68 peptides. Score 0.965 Round 5: 204 peptides, 2 chains. Longest chain 136 peptides. Score 0.971 Taking the results from Round 5 Chains 3, Residues 202, Estimated correctness of the model 100.0 % 2 chains (201 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 141 A 1 chains (204 residues) following loop building 1 chains (204 residues) in sequence following loop building ------------------------------------------------------ 32016 reflections ( 97.74 % complete ) and 1950 restraints for refining 2003 atoms. 318 conditional restraints added. Observations/parameters ratio is 4.00 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2822 (Rfree = 0.000) for 2003 atoms. Found 87 (155 requested) and removed 32 (77 requested) atoms. Cycle 7: After refmac, R = 0.2740 (Rfree = 0.000) for 2057 atoms. Found 67 (159 requested) and removed 6 (79 requested) atoms. Cycle 8: After refmac, R = 0.2680 (Rfree = 0.000) for 2117 atoms. Found 55 (164 requested) and removed 5 (82 requested) atoms. Cycle 9: After refmac, R = 0.2629 (Rfree = 0.000) for 2162 atoms. Found 56 (168 requested) and removed 2 (84 requested) atoms. Cycle 10: After refmac, R = 0.2598 (Rfree = 0.000) for 2213 atoms. Found 59 (172 requested) and removed 1 (86 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 1.47 1.57 Round 1: 201 peptides, 3 chains. Longest chain 69 peptides. Score 0.965 Round 2: 202 peptides, 2 chains. Longest chain 135 peptides. Score 0.970 Round 3: 201 peptides, 3 chains. Longest chain 68 peptides. Score 0.965 Round 4: 204 peptides, 1 chains. Longest chain 204 peptides. Score 0.976 Round 5: 201 peptides, 3 chains. Longest chain 69 peptides. Score 0.965 Taking the results from Round 4 Chains 1, Residues 203, Estimated correctness of the model 100.0 % 1 chains (203 residues) have been docked in sequence ------------------------------------------------------ 32016 reflections ( 97.74 % complete ) and 2102 restraints for refining 2130 atoms. 483 conditional restraints added. Observations/parameters ratio is 3.76 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2767 (Rfree = 0.000) for 2130 atoms. Found 86 (165 requested) and removed 28 (82 requested) atoms. Cycle 12: After refmac, R = 0.2671 (Rfree = 0.000) for 2186 atoms. Found 73 (169 requested) and removed 8 (84 requested) atoms. Cycle 13: After refmac, R = 0.2614 (Rfree = 0.000) for 2245 atoms. Found 78 (174 requested) and removed 4 (87 requested) atoms. Cycle 14: After refmac, R = 0.2586 (Rfree = 0.000) for 2314 atoms. Found 51 (180 requested) and removed 7 (90 requested) atoms. Cycle 15: After refmac, R = 0.2542 (Rfree = 0.000) for 2355 atoms. Found 80 (183 requested) and removed 3 (91 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 1.46 1.56 Round 1: 202 peptides, 3 chains. Longest chain 70 peptides. Score 0.965 Round 2: 202 peptides, 3 chains. Longest chain 83 peptides. Score 0.965 Round 3: 200 peptides, 4 chains. Longest chain 69 peptides. Score 0.958 Round 4: 202 peptides, 3 chains. Longest chain 85 peptides. Score 0.965 Round 5: 200 peptides, 4 chains. Longest chain 72 peptides. Score 0.958 Taking the results from Round 4 Chains 3, Residues 199, Estimated correctness of the model 99.9 % 3 chains (199 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 52 A and 55 A Built loop between residues 138 A and 141 A 1 chains (203 residues) following loop building 1 chains (203 residues) in sequence following loop building ------------------------------------------------------ 32016 reflections ( 97.74 % complete ) and 2227 restraints for refining 2255 atoms. 608 conditional restraints added. Observations/parameters ratio is 3.55 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2752 (Rfree = 0.000) for 2255 atoms. Found 106 (175 requested) and removed 29 (87 requested) atoms. Cycle 17: After refmac, R = 0.2667 (Rfree = 0.000) for 2327 atoms. Found 82 (181 requested) and removed 8 (90 requested) atoms. Cycle 18: After refmac, R = 0.2615 (Rfree = 0.000) for 2399 atoms. Found 54 (186 requested) and removed 7 (93 requested) atoms. Cycle 19: After refmac, R = 0.2561 (Rfree = 0.000) for 2444 atoms. Found 56 (189 requested) and removed 4 (94 requested) atoms. Cycle 20: After refmac, R = 0.2523 (Rfree = 0.000) for 2493 atoms. Found 41 (193 requested) and removed 7 (96 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 1.43 1.53 Round 1: 201 peptides, 4 chains. Longest chain 69 peptides. Score 0.959 Round 2: 202 peptides, 3 chains. Longest chain 84 peptides. Score 0.965 Round 3: 203 peptides, 3 chains. Longest chain 138 peptides. Score 0.966 Round 4: 201 peptides, 3 chains. Longest chain 83 peptides. Score 0.965 Round 5: 202 peptides, 3 chains. Longest chain 86 peptides. Score 0.965 Taking the results from Round 3 Chains 3, Residues 200, Estimated correctness of the model 99.9 % 3 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 54 A and 57 A Built loop between residues 69 A and 72 A 1 chains (204 residues) following loop building 1 chains (204 residues) in sequence following loop building ------------------------------------------------------ 32016 reflections ( 97.74 % complete ) and 2426 restraints for refining 2375 atoms. 795 conditional restraints added. Observations/parameters ratio is 3.37 ------------------------------------------------------ Cycle 21: After refmac, R = 0.2840 (Rfree = 0.000) for 2375 atoms. Found 104 (184 requested) and removed 30 (92 requested) atoms. Cycle 22: After refmac, R = 0.2707 (Rfree = 0.000) for 2446 atoms. Found 75 (190 requested) and removed 9 (95 requested) atoms. Failed to save intermediate PDB Cycle 23: After refmac, R = 0.2626 (Rfree = 0.000) for 2506 atoms. Found 59 (194 requested) and removed 5 (97 requested) atoms. Cycle 24: After refmac, R = 0.2587 (Rfree = 0.000) for 2556 atoms. Found 48 (198 requested) and removed 5 (99 requested) atoms. Cycle 25: After refmac, R = 0.2587 (Rfree = 0.000) for 2589 atoms. Found 46 (201 requested) and removed 5 (100 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 1.45 1.55 Round 1: 202 peptides, 3 chains. Longest chain 69 peptides. Score 0.965 Round 2: 202 peptides, 4 chains. Longest chain 69 peptides. Score 0.960 Round 3: 202 peptides, 3 chains. Longest chain 83 peptides. Score 0.965 Round 4: 202 peptides, 4 chains. Longest chain 70 peptides. Score 0.960 Round 5: 201 peptides, 5 chains. Longest chain 71 peptides. Score 0.953 Taking the results from Round 3 Chains 3, Residues 199, Estimated correctness of the model 99.9 % 3 chains (199 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 53 A and 56 A Built loop between residues 137 A and 141 A 1 chains (204 residues) following loop building 1 chains (204 residues) in sequence following loop building ------------------------------------------------------ 32016 reflections ( 97.74 % complete ) and 2624 restraints for refining 2489 atoms. 993 conditional restraints added. Observations/parameters ratio is 3.22 ------------------------------------------------------ Cycle 26: After refmac, R = 0.2739 (Rfree = 0.000) for 2489 atoms. Found 120 (193 requested) and removed 31 (96 requested) atoms. Cycle 27: After refmac, R = 0.2690 (Rfree = 0.000) for 2574 atoms. Found 83 (200 requested) and removed 11 (100 requested) atoms. Cycle 28: After refmac, R = 0.2670 (Rfree = 0.000) for 2638 atoms. Found 76 (205 requested) and removed 6 (102 requested) atoms. Cycle 29: After refmac, R = 0.2590 (Rfree = 0.000) for 2703 atoms. Found 54 (210 requested) and removed 7 (105 requested) atoms. Cycle 30: After refmac, R = 0.2543 (Rfree = 0.000) for 2747 atoms. Found 53 (213 requested) and removed 9 (106 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 1.46 1.56 Round 1: 205 peptides, 3 chains. Longest chain 126 peptides. Score 0.967 Round 2: 201 peptides, 4 chains. Longest chain 70 peptides. Score 0.959 Round 3: 205 peptides, 3 chains. Longest chain 126 peptides. Score 0.967 Round 4: 205 peptides, 2 chains. Longest chain 135 peptides. Score 0.972 Round 5: 198 peptides, 6 chains. Longest chain 70 peptides. Score 0.945 Taking the results from Round 4 Chains 2, Residues 203, Estimated correctness of the model 100.0 % 2 chains (203 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 137 A and 140 A 1 chains (205 residues) following loop building 1 chains (205 residues) in sequence following loop building ------------------------------------------------------ 32016 reflections ( 97.74 % complete ) and 2816 restraints for refining 2618 atoms. 1172 conditional restraints added. Observations/parameters ratio is 3.06 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2772 (Rfree = 0.000) for 2618 atoms. Found 134 (203 requested) and removed 31 (101 requested) atoms. Cycle 32: After refmac, R = 0.2677 (Rfree = 0.000) for 2717 atoms. Found 93 (211 requested) and removed 9 (105 requested) atoms. Cycle 33: After refmac, R = 0.2615 (Rfree = 0.000) for 2795 atoms. Found 75 (217 requested) and removed 8 (108 requested) atoms. Cycle 34: After refmac, R = 0.2561 (Rfree = 0.000) for 2859 atoms. Found 62 (222 requested) and removed 5 (111 requested) atoms. Cycle 35: After refmac, R = 0.2524 (Rfree = 0.000) for 2912 atoms. Found 66 (226 requested) and removed 8 (113 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 1.44 1.54 Round 1: 201 peptides, 4 chains. Longest chain 82 peptides. Score 0.959 Round 2: 203 peptides, 3 chains. Longest chain 70 peptides. Score 0.966 Round 3: 196 peptides, 5 chains. Longest chain 70 peptides. Score 0.950 Round 4: 202 peptides, 4 chains. Longest chain 70 peptides. Score 0.960 Round 5: 196 peptides, 5 chains. Longest chain 70 peptides. Score 0.950 Taking the results from Round 2 Chains 3, Residues 200, Estimated correctness of the model 99.9 % 3 chains (200 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 70 A Built loop between residues 137 A and 140 A 1 chains (204 residues) following loop building 1 chains (204 residues) in sequence following loop building ------------------------------------------------------ 32016 reflections ( 97.74 % complete ) and 3173 restraints for refining 2760 atoms. 1542 conditional restraints added. Observations/parameters ratio is 2.90 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2873 (Rfree = 0.000) for 2760 atoms. Found 131 (214 requested) and removed 46 (107 requested) atoms. Cycle 37: After refmac, R = 0.2691 (Rfree = 0.000) for 2843 atoms. Found 105 (220 requested) and removed 6 (110 requested) atoms. Cycle 38: After refmac, R = 0.2575 (Rfree = 0.000) for 2935 atoms. Found 85 (228 requested) and removed 10 (114 requested) atoms. Cycle 39: After refmac, R = 0.2493 (Rfree = 0.000) for 3000 atoms. Found 93 (233 requested) and removed 5 (116 requested) atoms. Cycle 40: After refmac, R = 0.2469 (Rfree = 0.000) for 3082 atoms. Found 61 (239 requested) and removed 7 (119 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 1.41 1.51 Round 1: 200 peptides, 6 chains. Longest chain 70 peptides. Score 0.947 Round 2: 204 peptides, 4 chains. Longest chain 78 peptides. Score 0.961 Round 3: 204 peptides, 2 chains. Longest chain 140 peptides. Score 0.971 Round 4: 196 peptides, 6 chains. Longest chain 69 peptides. Score 0.944 Round 5: 202 peptides, 4 chains. Longest chain 70 peptides. Score 0.960 Taking the results from Round 3 Chains 2, Residues 202, Estimated correctness of the model 100.0 % 2 chains (202 residues) have been docked in sequence Building loops using Loopy2018 Built loop between residues 67 A and 70 A 1 chains (204 residues) following loop building 1 chains (204 residues) in sequence following loop building ------------------------------------------------------ 32016 reflections ( 97.74 % complete ) and 3541 restraints for refining 2895 atoms. 1910 conditional restraints added. Observations/parameters ratio is 2.76 ------------------------------------------------------ Cycle 41: After refmac, R = 0.2770 (Rfree = 0.000) for 2895 atoms. Found 145 (224 requested) and removed 51 (112 requested) atoms. Cycle 42: After refmac, R = 0.2659 (Rfree = 0.000) for 2983 atoms. Found 106 (232 requested) and removed 6 (116 requested) atoms. Cycle 43: After refmac, R = 0.2611 (Rfree = 0.000) for 3072 atoms. Found 85 (239 requested) and removed 16 (119 requested) atoms. Cycle 44: After refmac, R = 0.2528 (Rfree = 0.000) for 3135 atoms. Found 69 (243 requested) and removed 3 (121 requested) atoms. Cycle 45: After refmac, R = 0.2488 (Rfree = 0.000) for 3193 atoms. Found 62 (248 requested) and removed 11 (124 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 1.43 1.53 Round 1: 190 peptides, 6 chains. Longest chain 51 peptides. Score 0.938 Round 2: 193 peptides, 5 chains. Longest chain 61 peptides. Score 0.947 Round 3: 191 peptides, 6 chains. Longest chain 51 peptides. Score 0.939 Round 4: 192 peptides, 5 chains. Longest chain 51 peptides. Score 0.947 Round 5: 188 peptides, 9 chains. Longest chain 43 peptides. Score 0.914 Taking the results from Round 4 Last building cycle: Chain fragments will be rearranged Chains 5, Residues 187, Estimated correctness of the model 99.9 % 5 chains (187 residues) have been docked in sequence Sequence coverage is 99 % All DUM atoms will be removed Building loops using Loopy2018 Built loop between residues 34 A and 38 A Built loop between residues 84 A and 88 A Built loop between residues 129 A and 140 A Built loop between residues 189 A and 193 A 1 chains (206 residues) following loop building 1 chains (206 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. Update only waters. 32016 reflections ( 97.74 % complete ) and 1651 restraints for refining 1614 atoms. Observations/parameters ratio is 4.96 ------------------------------------------------------ Cycle 46: After refmac, R = 0.3173 (Rfree = 0.000) for 1614 atoms. Found 21 (125 requested) and removed 0 (125 requested) atoms. Cycle 47: After refmac, R = 0.3004 (Rfree = 0.000) for 1614 atoms. Found 14 (126 requested) and removed 0 (63 requested) atoms. Cycle 48: After refmac, R = 0.2906 (Rfree = 0.000) for 1614 atoms. Found 5 (128 requested) and removed 0 (64 requested) atoms. Cycle 49: After refmac, R = 0.2824 (Rfree = 0.000) for 1614 atoms. Found 6 (128 requested) and removed 2 (64 requested) atoms. Writing output files ... TimeTaking 54.77